Title: Derivatives of the Diffusion Density and Cumulative Distribution
Function
Description: Calculates the partial derivative of the first-passage time diffusion probability density function (PDF) and cumulative distribution function (CDF)
with respect to the first-passage time t (only for PDF), the upper barrier a, the drift rate v, the relative starting point w, the non-decision time t0,
the inter-trial variability of the drift rate sv, the inter-trial variability of the rel. starting point sw, and the inter-trial variability of the
non-decision time st0. In addition the PDF and CDF themselves are also provided. Most calculations are done on the logarithmic scale to make it more stable.
Since the PDF, CDF, and their derivatives are represented as infinite series, we give the user the option to control the approximation errors with the argument
'precision'. For the numerical integration we used the C library cubature by Johnson, S. G. (2005-2013) <https://github.com/stevengj/cubature>. Numerical integration is
required whenever sv, sw, and/or st0 is not zero. Note that numerical integration reduces speed of the computation and the precision cannot be guaranteed
anymore. Therefore, whenever numerical integration is used an estimate of the approximation error is provided in the output list.
Author: Raphael Hartmann [aut, cre],
Karl C. Klauer [cph, aut, ctb, ths],
Steven G. Johnson [ctb],
Jean M. Linhart [ctb],
Brian Gough [ctb],
Gerard Jungman [ctb],
Rudolf Schuerer [ctb],
Przemyslaw Sliwa [ctb],
Jason H. Stover [ctb]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between WienR versions 0.1-9 dated 2021-05-07 and 0.2-0 dated 2021-05-11
DESCRIPTION | 17 + MD5 | 106 +++++------ R/WienerDens.R | 51 ++--- R/WienerDist.R | 45 ++--- R/daWienerDens.R | 47 ++--- R/daWienerDist.R | 49 ++--- R/dst0WienerDens.R | 7 R/dst0WienerDist.R | 7 R/dsvWienerDens.R | 7 R/dsvWienerDist.R | 7 R/dswWienerDens.R | 7 R/dswWienerDist.R | 7 R/dt0WienerDens.R | 9 - R/dt0WienerDist.R | 57 +++--- R/dtWienerDens.R | 49 ++--- R/dvWienerDens.R | 49 ++--- R/dvWienerDist.R | 49 ++--- R/dwWienerDens.R | 9 - R/dwWienerDist.R | 49 ++--- R/dxWienerDens.R | 9 - R/dxWienerDist.R | 9 - man/WienerCDF.Rd | 5 man/WienerPDF.Rd | 3 man/daWienerCDF.Rd | 5 man/daWienerPDF.Rd | 5 man/dst0WienerCDF.Rd | 5 man/dst0WienerPDF.Rd | 5 man/dsvWienerCDF.Rd | 5 man/dsvWienerPDF.Rd | 5 man/dswWienerCDF.Rd | 5 man/dswWienerPDF.Rd | 5 man/dt0WienerCDF.Rd | 5 man/dt0WienerPDF.Rd | 5 man/dtWienerPDF.Rd | 5 man/dvWienerCDF.Rd | 5 man/dvWienerPDF.Rd | 5 man/dwWienerCDF.Rd | 5 man/dwWienerPDF.Rd | 5 man/gradWienerCDF.Rd | 5 man/gradWienerPDF.Rd | 5 src/R_wrapper.cpp | 356 ++++++++++++++++++++++++++++++++++++++-- src/WienR_init.c | 4 src/adaptive_rejection_samp.cpp | 2 src/adaptive_rejection_samp.h | 1 src/cdf_fncs.cpp | 8 src/derivs.cpp | 121 +++++++------ src/derivs.h | 8 src/fncs_seven.cpp | 6 src/fncs_seven.h | 4 src/hcubature.c | 14 - src/rwiener.cpp | 48 +++-- src/rwiener.h | 2 src/tools.cpp | 1 src/tools.h | 19 +- 54 files changed, 877 insertions(+), 456 deletions(-)
Title: Nonparametric Estimation of the Trend and Its Derivatives in TS
Description: The nonparametric trend and its derivatives in equidistant time
series (TS) with short-memory stationary errors can be estimated. The
estimation is conducted via local polynomial regression using an
automatically selected bandwidth obtained by a built-in iterative plug-in
algorithm or a bandwidth fixed by the user. A Nadaraya-Watson kernel
smoother is also built-in as a comparison. With version 1.1.0, a linearity
test for the trend function, forecasting methods and backtesting
approaches are implemented as well.
The smoothing methods of the package are described in Feng, Y., Gries, T.,
and Fritz, M. (2020) <doi:10.1080/10485252.2020.1759598>.
Author: Yuanhua Feng [aut] (Paderborn University, Germany),
Sebastian Letmathe [aut] (Paderborn University, Germany),
Dominik Schulz [aut, cre] (Paderborn University, Germany),
Thomas Gries [ctb] (Paderborn University, Germany),
Marlon Fritz [ctb] (Paderborn University, Germany)
Maintainer: Dominik Schulz <schulzd@mail.uni-paderborn.de>
Diff between smoots versions 1.0.1 dated 2019-12-02 and 1.1.0 dated 2021-05-11
DESCRIPTION | 31 - MD5 | 104 +++-- NAMESPACE | 19 NEWS.md | 26 + R/RcppExports.R |only R/Welcome.R | 10 R/algorithms.R | 2 R/bootCast.R |only R/cf0.LW.est.R | 71 --- R/col.alpha.R |only R/color.name.R |only R/confBounds.R |only R/critMatrix.R |only R/dsmooth.R | 290 +++++++++------ R/fitted.R |only R/gdpUS.R | 2 R/gsmooth.R | 251 +++++++------ R/knsmooth.R | 97 +++-- R/maInfty.R |only R/modelCast.R |only R/msmooth.R | 418 +++++++++++++-------- R/msmoothCalc.R |only R/normCast.R |only R/optOrd.R |only R/plot.smoots.R | 277 ++++++++++---- R/print.smoots.R | 105 ++++- R/rescale.R |only R/residuals.R |only R/rollCast.R |only R/smoots.R | 132 +++++- R/sysdata.rda |binary R/tempNH.R | 4 R/trendCast.R |only R/tsmooth.R | 652 ++++++++++++++------------------- R/tsmoothCalc.R |only README.md | 188 ++++++--- man/bootCast.Rd |only man/confBounds.Rd |only man/critMatrix.Rd |only man/dax.Rd | 64 +-- man/dsmooth.Rd | 425 ++++++++++++---------- man/figures/README-confbounds-1.pdf |only man/figures/README-confbounds-1.png |only man/figures/README-fcast-1.pdf |only man/figures/README-fcast-1.png |only man/figures/README-plot1-1.pdf |only man/figures/README-plot1-1.png |binary man/figures/README-plot1-2.pdf |only man/figures/README-plot1-2.png |binary man/fitted.smoots.Rd |only man/gdpUS.Rd | 56 +- man/gsmooth.Rd | 343 +++++++++-------- man/knsmooth.Rd | 222 +++++------ man/modelCast.Rd |only man/msmooth.Rd | 650 +++++++++++++++++---------------- man/normCast.Rd |only man/optOrd.Rd |only man/plot.smoots.Rd | 76 +-- man/print.smoots.Rd | 54 +- man/rescale.Rd |only man/residuals.smoots.Rd |only man/rollCast.Rd |only man/smoots.Rd | 228 +++++++---- man/tempNH.Rd | 56 +- man/trendCast.Rd |only man/tsmooth.Rd | 695 +++++++++++++++++++----------------- man/vix.Rd | 64 +-- src |only 68 files changed, 3162 insertions(+), 2450 deletions(-)
Title: Optimal Project Prioritization
Description: A decision support tool for prioritizing conservation projects.
Prioritizations can be developed by maximizing expected feature richness,
expected phylogenetic diversity, the number of features that meet
persistence targets, or identifying a set of projects that meet persistence
targets for minimal cost. Constraints (e.g. lock in specific actions) and
feature weights can also be specified to further customize prioritizations.
After defining a project prioritization problem, solutions can be obtained
using exact algorithms, heuristic algorithms, or random processes. In
particular, it is recommended to install the 'Gurobi' optimizer (available
from <https://www.gurobi.com>) because it can identify optimal solutions
very quickly. Finally, methods are provided for comparing different
prioritizations and evaluating their benefits. For more information, see
Hanson et al. (2019) <doi:10.1111/2041-210X.13264>.
Author: Jeffrey O Hanson [aut, cre] (<https://orcid.org/0000-0002-4716-6134>),
Richard Schuster [aut] (<https://orcid.org/0000-0003-3191-7869>),
Matthew Strimas-Mackey [aut] (<https://orcid.org/0000-0001-8929-7776>),
Joseph R Bennett [aut] (<https://orcid.org/0000-0002-3901-9513>)
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between oppr versions 1.0.2 dated 2020-05-20 and 1.0.3 dated 2021-05-11
DESCRIPTION | 18 MD5 | 324 ++--- NEWS.md | 48 R/ArrayParameter-proto.R | 56 R/Collection-proto.R | 46 R/Constraint-proto.R | 8 R/Decision-proto.R | 8 R/Id.R | 6 R/MiscParameter-proto.R | 34 R/Objective-proto.R | 6 R/OptimizationProblem-methods.R | 58 R/OptimizationProblem-proto.R | 94 - R/Parameter-proto.R | 36 R/Parameters-proto.R | 48 R/ProjectModifier-proto.R | 90 - R/ProjectProblem-proto.R | 210 +-- R/ScalarParameter-proto.R | 46 R/Solver-proto.R | 28 R/Target-proto.R | 6 R/Weight-proto.R | 6 R/action_names.R | 4 R/add_absolute_targets.R | 26 R/add_binary_decisions.R | 12 R/add_default_solver.R | 24 R/add_feature_weights.R | 20 R/add_gurobi_solver.R | 100 - R/add_heuristic_solver.R | 35 R/add_locked_in_constraints.R | 32 R/add_locked_out_constraints.R | 6 R/add_lpsolveapi_solver.R | 28 R/add_lpsymphony_solver.R | 31 R/add_manual_locked_constraints.R | 20 R/add_manual_targets.R | 38 R/add_max_phylo_div_objective.R | 40 R/add_max_richness_objective.R | 26 R/add_max_targets_met_objective.R | 45 R/add_min_set_objective.R | 24 R/add_random_solver.R | 10 R/add_relative_targets.R | 9 R/add_rsymphony_solver.R | 33 R/branch_matrix.R | 10 R/compile.R | 10 R/constraints.R | 16 R/data.R | 116 - R/decisions.R | 10 R/feature_names.R | 4 R/internal.R | 57 R/magrittr-operators.R | 8 R/misc.R | 2 R/new_optimization_problem.R | 6 R/number_of_actions.R | 6 R/number_of_features.R | 6 R/number_of_projects.R | 6 R/objectives.R | 54 R/package.R | 38 R/parameters.R | 84 - R/plot.R | 26 R/plot_feature_persistence.R | 10 R/plot_phylo_persistence.R | 28 R/pproto.R | 12 R/predefined_optimization_problem.R | 46 R/print.R | 2 R/problem.R | 88 - R/project_cost_effectiveness.R | 22 R/project_names.R | 4 R/rake_phylogeny.R | 10 R/replacement_costs.R | 40 R/show.R | 2 R/simulate_ppp_data.R | 120 - R/simulate_ptm_data.R | 157 +- R/solution_statistics.R | 30 R/solve.R | 44 R/solvers.R | 42 R/star_phylogeny.R | 8 R/targets.R | 24 R/tbl_df.R | 12 R/waiver.R | 8 R/weights.R | 12 R/zzz.R | 1 README.md | 161 ++ build/vignette.rds |binary inst/doc/oppr.Rmd | 18 inst/doc/oppr.html | 1668 ++++++++++++++------------- man/ArrayParameter-class.Rd | 24 man/Collection-class.Rd | 20 man/Constraint-class.Rd | 6 man/Decision-class.Rd | 6 man/MiscParameter-class.Rd | 16 man/Objective-class.Rd | 4 man/OptimizationProblem-class.Rd | 12 man/OptimizationProblem-methods.Rd | 32 man/Parameter-class.Rd | 12 man/Parameters-class.Rd | 18 man/ProjectModifier-class.Rd | 46 man/ProjectProblem-class.Rd | 118 - man/ScalarParameter-class.Rd | 20 man/Solver-class.Rd | 14 man/Target-class.Rd | 6 man/Weight-class.Rd | 6 man/action_names.Rd | 2 man/add_absolute_targets.Rd | 56 man/add_binary_decisions.Rd | 20 man/add_default_solver.Rd | 24 man/add_feature_weights.Rd | 64 - man/add_gurobi_solver.Rd | 73 - man/add_heuristic_solver.Rd | 197 +-- man/add_locked_in_constraints.Rd | 50 man/add_locked_out_constraints.Rd | 6 man/add_lpsolveapi_solver.Rd | 45 man/add_lsymphony_solver.Rd | 51 man/add_manual_locked_constraints.Rd | 30 man/add_manual_targets.Rd | 72 - man/add_max_phylo_div_objective.Rd | 206 +-- man/add_max_richness_objective.Rd | 118 - man/add_max_targets_met_objective.Rd | 167 +- man/add_min_set_objective.Rd | 138 +- man/add_random_solver.Rd | 58 man/add_relative_targets.Rd | 59 man/add_rsymphony_solver.Rd | 45 man/array_parameters.Rd | 20 man/as.list.Rd | 4 man/branch_matrix.Rd | 8 man/compile.Rd | 12 man/constraints.Rd | 24 man/decisions.Rd | 18 man/feature_names.Rd | 2 man/figures/README-readme-plot-1.png |binary man/matrix_parameters.Rd | 2 man/misc_parameter.Rd | 2 man/new_id.Rd | 4 man/new_optimization_problem.Rd | 6 man/number_of_actions.Rd | 4 man/number_of_features.Rd | 4 man/number_of_projects.Rd | 4 man/objectives.Rd | 66 - man/oppr.Rd | 50 man/parameters.Rd | 6 man/pipe.Rd | 4 man/plot.ProjectProblem.Rd | 48 man/plot_feature_persistence.Rd | 34 man/plot_phylo_persistence.Rd | 48 man/print.Rd | 2 man/problem.Rd | 100 - man/project_cost_effectiveness.Rd | 54 man/project_names.Rd | 2 man/replacement_costs.Rd | 80 - man/scalar_parameters.Rd | 22 man/show.Rd | 2 man/sim_data.Rd | 135 -- man/simulate_ppp_data.Rd | 206 +-- man/simulate_ptm_data.Rd | 209 +-- man/solution_statistics.Rd | 40 man/solve.Rd | 90 - man/solvers.Rd | 114 - man/targets.Rd | 46 man/tee.Rd | 4 man/tibble-methods.Rd | 18 man/weights.Rd | 16 tests/testthat/helper_functions.R | 6 tests/testthat/test_decisions.R | 2 tests/testthat/test_plot.R | 1 tests/testthat/test_plot_phylo_persistence.R | 4 vignettes/oppr.Rmd | 18 163 files changed, 4112 insertions(+), 4037 deletions(-)
Title: Multivariate Kernel Density Estimation with Vine Copulas
Description: Implements the vine copula based kernel density estimator of
Nagler and Czado (2016) <doi:10.1016/j.jmva.2016.07.003>. The estimator does
not suffer from the curse of dimensionality and is therefore well suited for
high-dimensional applications.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between kdevine versions 0.4.2 dated 2018-12-17 and 0.4.3 dated 2021-05-11
DESCRIPTION | 10 +- MD5 | 12 +-- NEWS.md | 10 ++ R/kdevine-package.R | 2 R/kdevinecop.R | 1 R/structure_select2.R | 1 README.md | 168 ++++++++++++++++++++++++++++++-------------------- 7 files changed, 122 insertions(+), 82 deletions(-)
Title: Analytical Tool for Aquatic Respirometry
Description: Calculates metabolic rate of fish and other aquatic organisms measured using
an intermittent-flow respirometry approach. The tool is used to run a set of graphical
QC tests of raw respirometry data, correct it for background respiration and chamber
effect, filter and extract target values of absolute and mass-specific metabolic rate.
Experimental design should include background respiration tests and measuring of one
or more metabolic rate traits. The R package is ideally integrated with the pump
controller 'PumpResp' and the DO meter 'SensResp' (open-source hardware by FishResp).
Raw respirometry data can be also imported from 'AquaResp' (free software), 'AutoResp'
('LoligoSystems'), 'OxyView' ('PreSens'), 'Pyro Oxygen Logger' ('PyroScience') and
'Q-box Aqua' ('QubitSystems'). More information about the R package 'FishResp'is
available in the publication by Morozov et al. (2019) <doi:10.1093/conphys/coz003>.
Author: Sergey Morozov [aut, cre],
Scott McCairns [aut, ths],
Juha Merila [ths],
Federico Calboli [ctb],
Jenni Prokkola [dtc],
Stephen White [dtc],
Daniel Montgomery [dtc],
Laura Almodovar-Acevedo [dtc],
Niclas Kolm [dtc],
Alexander Kotrschal [dtc],
Erik Gill [dtc]
Maintainer: Sergey Morozov <sergey.morozov@helsinki.fi>
Diff between FishResp versions 1.0.3 dated 2019-03-07 and 1.1.0 dated 2021-05-11
DESCRIPTION | 37 +++++++++++++--------- MD5 | 71 ++++++++++++++++++++++++-------------------- NAMESPACE | 3 + NEWS.md |only R/FishResp.R | 2 - R/QC.activity.R | 1 R/QC.slope.R | 6 +-- R/convert.rMR.R | 3 + R/convert.respirometry.R | 3 + R/export.MR.R | 2 + R/extract.slope.R | 6 +-- R/prepare.data.R |only R/presens.aquaresp.R | 17 ++++++++-- R/pyroscience.aquaresp.R | 16 ++++++--- R/pyroscience.pumpresp.R |only README.md |only inst/extdata/amphipod |only inst/extdata/salmon |only man/AMR.Rd | 6 ++- man/AMR.clean.Rd | 6 ++- man/AMR.raw.Rd | 6 ++- man/AMR.slope.Rd | 6 ++- man/FishResp.Rd | 3 - man/QC.slope.Rd | 2 - man/SMR.Rd | 6 ++- man/SMR.clean.Rd | 6 ++- man/SMR.raw.Rd | 6 ++- man/SMR.slope.Rd | 6 ++- man/convert.rMR.Rd | 3 + man/convert.respirometry.Rd | 3 + man/export.MR.Rd | 2 + man/extract.slope.Rd | 2 - man/info.Rd | 6 ++- man/post.Rd | 6 ++- man/pre.Rd | 6 ++- man/prepare.data.Rd |only man/presens.aquaresp.Rd | 7 ++-- man/pyroscience.aquaresp.Rd | 10 +++--- man/pyroscience.pumpresp.Rd |only man/results.Rd | 6 ++- 40 files changed, 168 insertions(+), 103 deletions(-)
Title: Estimation Methods for Markets in Equilibrium and Disequilibrium
Description: Provides estimation methods for markets in equilibrium and
disequilibrium. Supports the estimation of an equilibrium and
four disequilibrium models with both correlated and independent shocks.
Also provides post-estimation analysis tools, such as aggregation,
marginal effect, and shortage calculations. The estimation methods are
based on full information maximum likelihood techniques given in
Maddala and Nelson (1974) <doi:10.2307/1914215>. They are implemented
using the analytic derivative expressions calculated in
Karapanagiotis (2020) <doi:10.2139/ssrn.3525622>. Standard
errors can be estimated by adjusting for heteroscedasticity or clustering.
The equilibrium estimation constitutes a case of a system of linear,
simultaneous equations. Instead, the disequilibrium models replace the
market-clearing condition with a non-linear,
short-side rule and allow for different specifications of price dynamics.
Author: Pantelis Karapanagiotis [aut, cre]
(<https://orcid.org/0000-0001-9871-1908>)
Maintainer: Pantelis Karapanagiotis <pikappa.devel@gmail.com>
Diff between diseq versions 0.2.1 dated 2021-04-14 and 0.3.1 dated 2021-05-11
diseq-0.2.1/diseq/man/aggregate_demand.Rd |only diseq-0.2.1/diseq/man/aggregate_supply.Rd |only diseq-0.2.1/diseq/man/demand_descriptives.Rd |only diseq-0.2.1/diseq/man/demanded_quantities.Rd |only diseq-0.2.1/diseq/man/diseq_basic-class.Rd |only diseq-0.2.1/diseq/man/diseq_deterministic_adjustment-class.Rd |only diseq-0.2.1/diseq/man/diseq_directional-class.Rd |only diseq-0.2.1/diseq/man/diseq_stochastic_adjustment-class.Rd |only diseq-0.2.1/diseq/man/disequilibrium_model-class.Rd |only diseq-0.2.1/diseq/man/equation_base-class.Rd |only diseq-0.2.1/diseq/man/equation_basic-class.Rd |only diseq-0.2.1/diseq/man/equation_deterministic_adjustment-class.Rd |only diseq-0.2.1/diseq/man/equation_directional-class.Rd |only diseq-0.2.1/diseq/man/equation_stochastic_adjustment-class.Rd |only diseq-0.2.1/diseq/man/equilibrium_model-class.Rd |only diseq-0.2.1/diseq/man/has_shortage.Rd |only diseq-0.2.1/diseq/man/marginal_effect_at_mean.Rd |only diseq-0.2.1/diseq/man/market_model-class.Rd |only diseq-0.2.1/diseq/man/mean_marginal_effect.Rd |only diseq-0.2.1/diseq/man/model_description.Rd |only diseq-0.2.1/diseq/man/normalized_shortages.Rd |only diseq-0.2.1/diseq/man/prefixed_const_variable.Rd |only diseq-0.2.1/diseq/man/prefixed_control_variables.Rd |only diseq-0.2.1/diseq/man/prefixed_independent_variables.Rd |only diseq-0.2.1/diseq/man/prefixed_price_variable.Rd |only diseq-0.2.1/diseq/man/prefixed_variance_variable.Rd |only diseq-0.2.1/diseq/man/relative_shortages.Rd |only diseq-0.2.1/diseq/man/shortage_probabilities.Rd |only diseq-0.2.1/diseq/man/simulate_model_data.Rd |only diseq-0.2.1/diseq/man/supplied_quantities.Rd |only diseq-0.2.1/diseq/man/supply_descriptives.Rd |only diseq-0.3.1/diseq/DESCRIPTION | 8 diseq-0.3.1/diseq/MD5 | 166 - 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Title: Bootstrap cis-QTL Method that Corrects for the Winner's Curse
Description: Identifies genome-related molecular traits with significant
evidence of genetic regulation and performs a bootstrap procedure to
correct estimated effect sizes for over-estimation present in cis-QTL
mapping studies (The "Winner's Curse"), described in Huang QQ *et al.*
2018 <doi: 10.1093/nar/gky780>.
Author: Qin Qin Huang [aut],
Scott Ritchie [aut, cre]
Maintainer: Scott Ritchie <sritchie73@gmail.com>
Diff between BootstrapQTL versions 1.0.2 dated 2018-09-21 and 1.0.5 dated 2021-05-11
DESCRIPTION | 9 ++---- MD5 | 8 ++--- R/BootstrapQTL.R | 75 ++++++++++++++++++++++++++------------------------ R/utils.R | 12 +------- tests/testthat/test.R | 35 ++++++++++++++++++----- 5 files changed, 77 insertions(+), 62 deletions(-)
Title: Bayesian Aggregate Treatment Effects
Description: Running and comparing meta-analyses of data with hierarchical
Bayesian models in Stan, including convenience functions for formatting
data, plotting and pooling measures specific to meta-analysis. This implements many models
from Meager (2019) <doi:10.1257/app.20170299>.
Author: Witold Wiecek [cre, aut],
Rachael Meager [aut],
Brice Green [ctb] (predict(), loo_compare, many visuals),
Trustees of Columbia University [cph] (tools/make_cc.R)
Maintainer: Witold Wiecek <witold.wiecek@gmail.com>
Diff between baggr versions 0.4.0 dated 2020-02-28 and 0.6.4 dated 2021-05-11
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baggr-0.6.4/baggr/vignettes/baggr.bib | 41 + baggr-0.6.4/baggr/vignettes/baggr_binary.Rmd | 291 ++++--- 122 files changed, 3771 insertions(+), 2497 deletions(-)
Title: Design of Experiments Suite: Generate and Evaluate Optimal
Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of blocked and split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible.
Author: Tyler Morgan-Wall [aut, cre],
George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between skpr versions 0.64.2 dated 2020-03-04 and 0.66.5 dated 2021-05-11
DESCRIPTION | 17 MD5 | 107 +- NAMESPACE | 6 R/RcppExports.R | 16 R/calc_interaction_degrees.R | 11 R/calculate_degrees_of_freedom.R | 3 R/effectpower.R | 12 R/eval_design.R | 18 R/eval_design_custom_mc.R | 7 R/eval_design_mc.R | 53 + R/eval_design_survival_mc.R | 2 R/gen_design.R | 398 ++++------ R/get_optimality.R | 10 R/methods.R | 39 - R/parallel_search_progress.R |only R/parameterpower.R | 12 R/plot_fds.R | 7 R/skprGUI.R | 465 +++++------- R/skprGUIserver.R | 271 ++++-- README.md | 207 +++-- inst/shiny/skprGUI/server.R | 571 ++++++-------- inst/shiny/skprGUI/ui.R | 758 +++++++++---------- man/aliasmodel.Rd | 34 man/blockingstructure.Rd | 34 man/calcblocksizes.Rd | 38 man/disallowed_combinations.Rd | 34 man/gen_anticoef.Rd | 42 - man/gen_design.Rd | 652 ++++++++-------- man/generate_noise_block.Rd | 34 man/get_optimality.Rd | 2 man/normalize_numeric_runmatrix.Rd | 34 man/permutations.Rd | 34 man/pipe.Rd | 14 man/plot_fds.Rd | 100 +- man/potential_permuted_factors.Rd | 34 man/print.skpr_eval_output.Rd | 7 man/priorlevels.Rd | 36 man/quad.Rd | 34 man/rearrange_formula_by_order.Rd | 34 man/reduceRunMatrix.Rd | 38 man/remove_skpr_blockcols.Rd | 34 man/skprGUI.Rd | 38 man/skprGUIbrowser.Rd | 28 man/skprGUIserver.Rd | 38 src/Makevars | 1 src/Makevars.win | 2 src/RcppExports.cpp | 55 + src/coord_exchange_functions.h |only src/exported_optimality.cpp | 2 src/genOptimalDesign.cpp | 1433 ------------------------------------- src/genOptimalDesignCoord.cpp |only src/genSplitPlotOptimalDesign.cpp |only src/getBlockedOptimalDesign.cpp |only src/nullify_alg.h | 2 src/optimalityfunctions.cpp | 2 tests/testthat/Rplots.pdf |binary tests/testthat/testExampleCode.R | 7 57 files changed, 2316 insertions(+), 3551 deletions(-)
Title: Using Percolation and Conductance to Find Information Flow
Certainty in a Direct Network
Description: To find the certainty of dominance interactions with indirect
interactions being considered.
Author: Kevin Fujii [aut],
Jian Jin [aut],
Jessica Vandeleest [aut, cre],
Aaron Shev [aut],
Brianne Beisner [aut],
Brenda McCowan [aut, cph],
Hsieh Fushing [aut, cph]
Maintainer: Jessica Vandeleest <vandelee@ucdavis.edu>
Diff between Perc versions 0.1.5 dated 2020-04-27 and 0.1.6 dated 2021-05-11
DESCRIPTION | 13 - MD5 | 18 - R/Perc.R | 2 build/vignette.rds |binary inst/doc/Perc.R | 42 +-- inst/doc/Perc.html | 458 +++++++++++++----------------------------- man/Perc.Rd | 2 man/sampleEdgelist.Rd | 6 man/sampleRawMatrix.Rd | 6 man/sampleWeightedEdgelist.Rd | 6 10 files changed, 197 insertions(+), 356 deletions(-)
Title: Simultaneous Confidence Intervals for Multinomial Proportions
According to the Method by Sison and Glaz
Description: An implementation of a method for building simultaneous confidence intervals for the probabilities of a multinomial distribution given a set of observations, proposed by Sison and Glaz in their paper:
Sison, C.P and J. Glaz. Simultaneous confidence intervals and sample size determination for multinomial proportions. Journal of the American Statistical Association, 90:366-369 (1995).
The method is an R translation of the SAS code implemented by May and Johnson in their paper:
May, W.L. and W.D. Johnson. Constructing two-sided simultaneous confidence intervals for multinomial proportions for small counts in a large number of cells. Journal of Statistical Software 5(6) (2000).
Paper and code available at <DOI:10.18637/jss.v005.i06>.
Author: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Maintainer: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Diff between MultinomialCI versions 1.1 dated 2019-09-07 and 1.2 dated 2021-05-11
DESCRIPTION | 14 +++--- MD5 | 8 +-- NAMESPACE | 4 - R/sison.R | 44 ++++++++++++++++++- man/multinomialCI.Rd | 114 +++++++++++++++++++++++---------------------------- 5 files changed, 108 insertions(+), 76 deletions(-)
Title: R Interface for the C Implementation of CEC Benchmark Functions
Description: Goal of this package is to provide access to benchmark functions defined for
the Special Session and Competition on Real-Parameter Single Objective Optimization in one place.
The package contains functions from following years: 2013, 2014, 2015,
2017, 2019, 2021 (<https://github.com/P-N-Suganthan>).
Implementations of CEC-2013 (Y. Gonzalez-Fernandez & M. Zambrano-Bigiarini) and CEC2017 (D. Jagodziński) are taken from existed R packages. Also,
the original C source code has been cleaned and reorganized for better readability.
Author: Eryk Warchulski [aut, cre],
Dariusz Jagodziński [cph],
Yasser Gonzalez-Fernandez [cph],
Mauricio Zambrano-Bigiarini [cph]
Maintainer: Eryk Warchulski <ewarchul@gmail.com>
Diff between cecs versions 0.2.0 dated 2021-04-25 and 0.2.1 dated 2021-05-11
DESCRIPTION | 6 +-- MD5 | 7 ++-- NEWS.md |only R/utils.R | 3 + README.md | 104 +++--------------------------------------------------------- 5 files changed, 15 insertions(+), 105 deletions(-)
Title: Weighted Mixed-Effects Models Using Multilevel Pseudo Maximum
Likelihood Estimation
Description: Run mixed-effects models that include weights at every level. The WeMix package fits a weighted mixed model, also known as a multilevel, mixed, or hierarchical linear model (HLM). The weights could be inverse selection probabilities, such as those developed for an education survey where schools are sampled probabilistically, and then students inside of those schools are sampled probabilistically. Although mixed-effects models are already available in R, WeMix is unique in implementing methods for mixed models using weights at multiple levels. Both linear and logit models are supported. Models may have up to three levels.
Author: Emmanuel Sikali [pdr],
Paul Bailey [aut, cre],
Claire Kelley [aut],
Trang Nguyen [aut],
Huade Huo [aut],
Eric Buehler [ctb],
Christian Kjeldsen [ctb]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between WeMix versions 3.1.6 dated 2020-12-08 and 3.1.7 dated 2021-05-11
DESCRIPTION | 31 ++++- MD5 | 16 +- R/adaptiveQuad.R | 13 +- R/helpers.R | 26 +++- build/vignette.rds |binary inst/NEWS.Rd | 8 + inst/doc/Introduction_to_Mixed_Effects_Models_With_WeMix.pdf |binary inst/doc/Weighted_Linear_Mixed_Effects_Models.pdf |binary tests/testthat/test-1-main.R | 59 +++++------ 9 files changed, 96 insertions(+), 57 deletions(-)
Title: Easily Access timsTOF Data
Description: Access 'timsTOF' mass spectrometry data, as described <https://sso.bruker.com/auth/realms/bruker/protocol/openid-connect/auth?client_id=aem-bruker.com&redirect_uri=https%3A%2F%2Fwww.bruker.com%2Fen.login.html%3FtargetUrl%3Dhttps%3A%2F%2Fwww.bruker.com%2Fen%2Fservices%2Fsoftware-downloads%2Fmass-spectrometry.html&response_type=id_token%20token&scope=openid%20profile&state=4f9d225e92f341cca3b03a55533dbd65&nonce=f550633b1e984ecfb07979ae6d9277b4&ui_locales=en> (after registering), using the 'OpenTIMS' C++ reader and save all into 'data.tables'.
Author: Mateusz Krzysztof Łącki [aut, cre, cph]
(<https://orcid.org/0000-0001-7415-4748>),
Michał Piotr Startek [aut, cph]
(<https://orcid.org/0000-0001-5227-3447>)
Maintainer: Mateusz Krzysztof Łącki <matteo.lacki@gmail.com>
Diff between timsr versions 0.0.2 dated 2021-05-04 and 0.0.3 dated 2021-05-11
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/timsr.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Fit a Spatial Occupancy Model via Gibbs Sampling
Description: Fit a spatial-temporal occupancy models using
a probit formulation instead of a traditional logit
model.
Author: Devin S. Johnson
Maintainer: Devin S. Johnson <devin.johnson@noaa.gov>
Diff between stocc versions 1.30 dated 2015-08-23 and 1.31 dated 2021-05-11
DESCRIPTION | 9 +++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 2 +- R/icar.Q.R | 11 +++++++++++ R/spatial.occupancy.R | 7 ++++--- R/stocc-package.R | 2 +- demo/simDataMCMC.R | 1 + man/habData.Rd | 18 +++++++++++------- man/icar.Q.Rd | 3 +-- man/make.so.data.Rd | 3 +-- man/occupancyData.Rd | 29 ++++++++++++++++------------- man/spatial.occupancy.Rd | 28 +++++++++++++++++----------- man/stocc-package.Rd | 7 +++---- man/visitData.Rd | 13 ++++++++----- 14 files changed, 93 insertions(+), 66 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>;
- net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>;
- measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>;
- ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>;
- partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Bruggemann, 2014) <DOI:10.1002/cem.2569>; (Rücker & Schwarzer, 2017) <DOI:10.1002/jrsm.1270>;
- split direct and indirect evidence to check consistency (Dias et al., 2010) <DOI:10.1002/sim.3767>, (Efthimiou et al., 2019) <DOI:10.1002/sim.8158>;
- league table with network meta-analysis results;
- additive network meta-analysis for combinations of treatments (Rücker et al., 2019) <DOI:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <DOI:10.1002/sim.8158>;
- 'comparison-adjusted' funnel plot (Chaimani & Salanti, 2012) <DOI:10.1002/jrsm.57>;
- automated drawing of network graphs described in Rücker & Schwarzer (2016) <DOI:10.1002/jrsm.1143>.
Author: Gerta Rücker [aut] (<https://orcid.org/0000-0002-2192-2560>),
Ulrike Krahn [aut],
Jochem König [aut] (<https://orcid.org/0000-0003-4683-0360>),
Orestis Efthimiou [aut] (<https://orcid.org/0000-0002-0955-7572>),
Guido Schwarzer [aut, cre] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 1.3-0 dated 2021-01-18 and 1.4-0 dated 2021-05-11
DESCRIPTION | 10 MD5 | 96 +- NAMESPACE | 4 NEWS.md | 91 + R/as.data.frame.netconnection.R |only R/as.data.frame.netmeta.R | 2 R/decomp.tau.R | 36 R/discomb.R | 207 +++- R/forest.netbind.R | 28 R/forest.netcomb.R | 4 R/forest.netmeta.R | 19 R/forest.netsplit.R | 2 R/multiarm.R | 4 R/netcomb.R | 2 R/netconnection.R | 187 +++ R/netgraph.netconnection.R | 21 R/netgraph.netmeta.R | 18 R/netheat.R | 41 R/netimpact.R | 12 R/netleague.R | 13 R/netmeasures.R | 48 - R/netmeta-internal.R | 46 R/netmeta-package.R | 6 R/netmeta.R | 347 ++++++- R/netsplit.R | 2 R/nma.additive.R | 3 R/nma.krahn.R | 11 R/nma.ruecker.R | 2 R/pairwise.R | 1767 ++++++++++++++++++++----------------- R/print.netmeta.R | 30 R/summary.netmeta.R | 14 man/as.data.frame.netconnection.Rd |only man/as.data.frame.netmeta.Rd | 2 man/discomb.Rd | 3 man/forest.netbind.Rd | 6 man/forest.netcomb.Rd | 4 man/forest.netmeta.Rd | 5 man/forest.netsplit.Rd | 2 man/netconnection.Rd | 7 man/netgraph.netconnection.Rd | 12 man/netgraph.netmeta.Rd | 4 man/netheat.Rd | 18 man/netimpact.Rd | 7 man/netleague.Rd | 12 man/netmeta-package.Rd | 4 man/netmeta.Rd | 51 - man/netsplit.Rd | 2 man/pairwise.Rd | 24 man/print.netmeta.Rd | 4 man/summary.netmeta.Rd | 4 50 files changed, 2181 insertions(+), 1063 deletions(-)
Title: Meta-Analysis of Diagnostic Accuracy Studies with Several
Cutpoints
Description: Provides methods by Steinhauser et al. (2016) <DOI:10.1186/s12874-016-0196-1> for meta-analysis of diagnostic accuracy studies with several cutpoints.
Author: Gerta Rücker [aut] (<https://orcid.org/0000-0002-2192-2560>),
Susanne Steinhauser [aut],
Srinath Kolampally [aut],
Guido Schwarzer [aut, cre] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between diagmeta versions 0.4-0 dated 2020-04-02 and 0.4-1 dated 2021-05-11
diagmeta-0.4-0/diagmeta/NEWS |only diagmeta-0.4-1/diagmeta/DESCRIPTION | 12 - diagmeta-0.4-1/diagmeta/MD5 | 16 +- diagmeta-0.4-1/diagmeta/NEWS.md |only diagmeta-0.4-1/diagmeta/R/diagmeta.R | 128 ++++++++++++++------- diagmeta-0.4-1/diagmeta/R/diagstats.R | 44 ++++--- diagmeta-0.4-1/diagmeta/R/plot.diagmeta.R | 8 - diagmeta-0.4-1/diagmeta/R/print.diagmeta.R | 2 diagmeta-0.4-1/diagmeta/R/print.summary.diagmeta.R | 2 diagmeta-0.4-1/diagmeta/man/diagmeta.Rd | 2 10 files changed, 138 insertions(+), 76 deletions(-)
Title: Helps You to Code Cleaner
Description: Check your R code for some of the most common
layout flaws. Many tried to teach us how to write code less dreadful,
be it implicitly as B. W. Kernighan and D. M. Ritchie (1988)
<ISBN:0-13-110362-8> in 'The C Programming Language' did, be it
explicitly as R.C. Martin (2008) <ISBN:0-13-235088-2> in 'Clean Code:
A Handbook of Agile Software Craftsmanship' did. So we should check
our code for files too long or wide, functions with too many lines,
too wide lines, too many arguments or too many levels of nesting.
Note: This is not a static code analyzer like pylint or the like.
Checkout <https://cran.r-project.org/package=lintr> instead.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between cleanr versions 1.3.1 dated 2020-11-20 and 1.3.2 dated 2021-05-11
DESCRIPTION | 9 -- MD5 | 48 ++++++----- NEWS.md | 4 R/checks.R | 6 - R/internals.R | 6 - R/options.R | 7 - R/utils.R | 67 +--------------- R/wrappers.R | 6 - build/cleanr.pdf |binary build/vignette.rds |binary inst/doc/cleanr_Introduction.html | 101 +++++++++---------------- inst/runit_tests/source/R_s4/AllConstructors.R | 2 inst/source/R/checks.R | 11 +- inst/source/R/internals.R | 6 - inst/source/R/options.R | 10 +- inst/source/R/utils.R | 6 - inst/source/R/wrappers.R | 26 +++--- inst/vignettes_code |only man/check_function_layout.Rd | 2 man/check_package.Rd | 2 man/function_checks.Rd | 2 man/get_cleanr_options.Rd | 3 man/is_not_false.Rd | 22 ----- man/load_internal_functions.Rd | 14 --- man/set_cleanr_options.Rd | 4 vignettes/sedscr |only 26 files changed, 142 insertions(+), 222 deletions(-)
Title: Calculate Power and Sample Size for Two Sample Mean Tests
Description: Power calculations are a critical component of any research study to determine the
minimum sample size necessary to detect differences between multiple groups. Here we
present an 'R' package, 'PASSED', that performs power and sample size calculations for
the test of two-sample means or ratios with data following beta,
gamma (Chang et al. (2011), <doi:10.1007/s00180-010-0209-1>), normal,
Poisson (Gu et al. (2008), <doi:10.1002/bimj.200710403>), binomial, geometric, and
negative binomial (Zhu and Lakkis (2014), <doi:10.1002/sim.5947>) distributions.
Author: Jinpu Li [aut, cre],
Ryan Knigge [aut],
Kaiyi Chen [aut],
Emily Leary [aut]
Maintainer: Jinpu Li <lijinp@health.missouri.edu>
Diff between PASSED versions 1.0-3 dated 2020-07-21 and 1.1-0 dated 2021-05-11
DESCRIPTION | 15 - MD5 | 32 +- NAMESPACE | 34 +- R/power_Beta.R | 556 ++++++++++++++++++++++-------------------- R/power_Binomial.R | 203 +++++++++------ R/power_Gamma.R | 240 +++++++++--------- R/power_Geometric.R | 174 +++++++------ R/power_NegativeBinomial.R | 175 +++++++------ R/power_Normal.R | 215 +++++++++------- R/power_Poisson.R | 144 ++++++---- man/power_Beta.Rd | 29 +- man/power_Binomial.Rd | 13 man/power_Gamma.Rd | 12 man/power_Geometric.Rd | 23 + man/power_NegativeBinomial.Rd | 24 + man/power_Normal.Rd | 18 - man/power_Poisson.Rd | 20 - 17 files changed, 1072 insertions(+), 855 deletions(-)
More information about TensorComplete at CRAN
Permanent link
Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and
writing data between R and other statistical software packages like 'SPSS',
'SAS' or 'Stata', and working with labelled data. This includes easy ways
to get, set or change value and variable label attributes, to convert
labelled vectors into factors or numeric (and vice versa), or to deal with
multiple declared missing values.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
avid Ranzolin [ctb],
Jonathan De Troye [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjlabelled versions 1.1.7 dated 2020-09-24 and 1.1.8 dated 2021-05-11
DESCRIPTION | 14 MD5 | 86 +-- NEWS.md | 13 R/add_labels.R | 8 R/as_factor.R | 109 ++-- R/as_label.R | 2 R/as_labelled.R | 62 ++ R/as_numeric.R | 6 R/convert_case.R | 2 R/copy_labels.R | 4 R/drop_labels.R | 2 R/fill_labels.R | 10 R/get_label.R | 6 R/get_model_labels.R | 21 R/get_na.R | 17 R/get_values.R | 2 R/helpfunctions.R | 2 R/label_to_colnames.R | 14 R/read.R | 21 R/remove_all_labels.R | 2 R/remove_labels.R | 8 R/set_labels.R | 264 ++++++----- R/set_na.R | 186 ++++---- R/tidy_labels.R | 51 +- R/val_labels.R | 2 R/var_labels.R | 2 R/write.R | 4 R/zap_labels.R | 161 +++---- build/vignette.rds |binary inst/doc/intro_sjlabelled.html | 927 +++++++++++++++++++++-------------------- inst/doc/labelleddata.R | 4 inst/doc/labelleddata.Rmd | 4 inst/doc/labelleddata.html | 199 +++++--- inst/doc/quasiquotation.html | 439 ++++++++++--------- man/as_factor.Rd | 73 +-- man/as_labelled.Rd | 12 man/get_na.Rd | 15 man/label_to_colnames.Rd | 8 man/set_labels.Rd | 232 +++++----- man/set_na.Rd | 165 +++---- man/term_labels.Rd | 21 man/tidy_labels.Rd | 30 - man/zap_labels.Rd | 154 +++--- vignettes/labelleddata.Rmd | 4 44 files changed, 1818 insertions(+), 1550 deletions(-)
Title: Analysis of Single-Cell Chromatin Data
Description: A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2020) <doi:10.1101/2020.11.09.373613>.
Author: Tim Stuart [aut, cre] (<https://orcid.org/0000-0002-3044-0897>),
Avi Srivastava [aut] (<https://orcid.org/0000-0001-9798-2079>),
Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>),
Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)
Maintainer: Tim Stuart <tstuart@nygenome.org>
Diff between Signac versions 1.2.0 dated 2021-04-28 and 1.2.1 dated 2021-05-11
DESCRIPTION | 8 - MD5 | 27 +++--- NAMESPACE | 1 NEWS.md | 14 +++ R/fragments.R | 26 ++++++ R/objects.R | 4 R/preprocessing.R | 9 +- build/partial.rdb |binary inst/extdata/fragments_header.tsv.gz |only inst/extdata/fragments_header.tsv.gz.tbi |only man/head.Fragment.Rd |only src/filter.cpp | 24 ++++- src/group.cpp | 25 +++++- src/split.cpp | 23 ++++- src/validate.cpp | 24 +++++ tests/testthat/test_fragments.R | 128 +++++++++++++++++++++++++++++++ 16 files changed, 281 insertions(+), 32 deletions(-)
More information about academictwitteR at CRAN
Permanent link
Title: Data from all Seasons of Survivor (US) TV Series in Tidy Format
Description: Several datasets which detail the results and events of each season of Survivor. This includes
details on the cast, voting history, immunity and reward challenges, jury votes and viewers. This data is
useful for practicing data wrangling, graph analytics and analysing how each season of Survivor played out.
Includes 'ggplot2' scales and colour palettes for visualisation.
Author: Daniel Oehm [aut, cre]
Maintainer: Daniel Oehm <danieloehm@gmail.com>
Diff between survivoR versions 0.9.2 dated 2021-04-06 and 0.9.3 dated 2021-05-11
DESCRIPTION | 9 - MD5 | 37 ++++--- NEWS.md |only R/datasets.R | 104 +++++++++++++++++++- README.md | 237 ++++++++++++++++++++++++----------------------- data/castaways.rda |binary data/challenges.rda |only data/hidden-idols.rda |only data/immunity.rda |binary data/jury-votes.rda |binary data/rewards.rda |binary data/season-palettes.rda |binary data/season-summary.rda |binary data/tribe-colours.rda |binary data/tribe-mapping.rda |only data/viewers.rda |binary data/vote-history.rda |binary man/challenges.Rd |only man/hidden_idols.Rd |only man/immunity.Rd | 5 man/rewards.Rd | 3 man/season_summary.Rd | 4 man/tribe_mapping.Rd |only 23 files changed, 257 insertions(+), 142 deletions(-)
Title: Kernel Density Estimation for Heaped and Rounded Data
Description: In self-reported or anonymised data the user often encounters
heaped data, i.e. data which are rounded (to a possibly different degree
of coarseness). While this is mostly a minor problem in parametric density
estimation the bias can be very large for non-parametric methods such as kernel
density estimation. This package implements a partly Bayesian algorithm treating
the true unknown values as additional parameters and estimates the rounding
parameters to give a corrected kernel density estimate. It supports various
standard bandwidth selection methods. Varying rounding probabilities (depending
on the true value) and asymmetric rounding is estimable as well: Gross, M. and Rendtel, U. (2016) (<doi:10.1093/jssam/smw011>).
Additionally, bivariate non-parametric density estimation for rounded data, Gross, M. et al. (2016) (<doi:10.1111/rssa.12179>),
as well as data aggregated on areas is supported.
Author: Marcus Gross [aut, cre],
Kerstin Erfurth [ctb]
Maintainer: Marcus Gross <marcus.gross@inwt-statistics.de>
Diff between Kernelheaping versions 2.2.2 dated 2020-02-21 and 2.2.8 dated 2021-05-11
DESCRIPTION | 12 +-- MD5 | 24 +++---- NAMESPACE | 2 R/functions.R | 132 +++++++++++++++++++++++++++++------------ man/Kernelheaping.Rd | 1 man/createSim.Kernelheaping.Rd | 12 +++ man/dbivr.Rd | 10 ++- man/dclass.Rd | 24 ++++--- man/dheaping.Rd | 19 ++++- man/dshapebivr.Rd | 16 ++++ man/dshapebivrProp.Rd | 16 ++++ man/sim.Kernelheaping.Rd | 22 +++++- man/toOtherShape.Rd | 2 13 files changed, 210 insertions(+), 82 deletions(-)
Title: Create Interactive Chart with the JavaScript 'ApexCharts'
Library
Description: Provides an 'htmlwidgets' interface to 'apexcharts.js'.
'Apexcharts' is a modern JavaScript charting library to build interactive charts and visualizations with simple API.
'Apexcharts' examples and documentation are available here: <https://apexcharts.com/>.
Author: Victor Perrier [aut, cre],
Fanny Meyer [aut],
Juned Chhipa [cph] (apexcharts.js library),
Mike Bostock [cph] (d3.format library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between apexcharter versions 0.1.8 dated 2020-11-18 and 0.2.0 dated 2021-05-11
apexcharter-0.1.8/apexcharter/inst/example-brush |only apexcharter-0.1.8/apexcharter/inst/example-brush-proxy |only apexcharter-0.1.8/apexcharter/inst/example-spark |only apexcharter-0.1.8/apexcharter/inst/example-sync |only apexcharter-0.1.8/apexcharter/inst/examples-input |only apexcharter-0.1.8/apexcharter/inst/examples-proxy |only apexcharter-0.1.8/apexcharter/inst/htmlwidgets/lib |only apexcharter-0.2.0/apexcharter/DESCRIPTION | 12 apexcharter-0.2.0/apexcharter/MD5 | 353 +++++----- apexcharter-0.2.0/apexcharter/NAMESPACE | 27 apexcharter-0.2.0/apexcharter/NEWS.md | 11 apexcharter-0.2.0/apexcharter/R/apex-options.R | 7 apexcharter-0.2.0/apexcharter/R/apex-utils.R | 92 +- apexcharter-0.2.0/apexcharter/R/apex.R | 105 ++ apexcharter-0.2.0/apexcharter/R/apexcharter-package.R | 12 apexcharter-0.2.0/apexcharter/R/apexcharter.R | 16 apexcharter-0.2.0/apexcharter/R/colors.R | 6 apexcharter-0.2.0/apexcharter/R/data.R | 2 apexcharter-0.2.0/apexcharter/R/facets.R |only apexcharter-0.2.0/apexcharter/R/format.R | 4 apexcharter-0.2.0/apexcharter/R/grid.R |only apexcharter-0.2.0/apexcharter/R/mixed-charts.R | 13 apexcharter-0.2.0/apexcharter/R/onLoad.R | 8 apexcharter-0.2.0/apexcharter/R/parse-data.R | 10 apexcharter-0.2.0/apexcharter/R/proxy.R | 82 +- apexcharter-0.2.0/apexcharter/R/shiny-input.R | 15 apexcharter-0.2.0/apexcharter/R/spark-box.R | 8 apexcharter-0.2.0/apexcharter/R/utils.R | 62 + apexcharter-0.2.0/apexcharter/README.md | 13 apexcharter-0.2.0/apexcharter/build/vignette.rds |binary apexcharter-0.2.0/apexcharter/inst/doc/apexcharter.R | 36 - apexcharter-0.2.0/apexcharter/inst/doc/apexcharter.Rmd | 38 - apexcharter-0.2.0/apexcharter/inst/doc/apexcharter.html | 225 ++---- apexcharter-0.2.0/apexcharter/inst/doc/chart-options.R | 26 apexcharter-0.2.0/apexcharter/inst/doc/chart-options.Rmd | 26 apexcharter-0.2.0/apexcharter/inst/doc/chart-options.html | 194 ++--- apexcharter-0.2.0/apexcharter/inst/doc/facets.R |only apexcharter-0.2.0/apexcharter/inst/doc/facets.Rmd |only apexcharter-0.2.0/apexcharter/inst/doc/facets.html |only apexcharter-0.2.0/apexcharter/inst/doc/shiny-integration.R | 6 apexcharter-0.2.0/apexcharter/inst/doc/shiny-integration.Rmd | 4 apexcharter-0.2.0/apexcharter/inst/doc/shiny-integration.html | 111 +-- apexcharter-0.2.0/apexcharter/inst/doc/spark-box.R | 1 apexcharter-0.2.0/apexcharter/inst/doc/spark-box.Rmd | 1 apexcharter-0.2.0/apexcharter/inst/doc/spark-box.html | 95 -- apexcharter-0.2.0/apexcharter/inst/doc/sync-charts.R | 41 + apexcharter-0.2.0/apexcharter/inst/doc/sync-charts.Rmd | 25 apexcharter-0.2.0/apexcharter/inst/doc/sync-charts.html | 134 +-- apexcharter-0.2.0/apexcharter/inst/examples/brush |only apexcharter-0.2.0/apexcharter/inst/examples/brush-proxy |only apexcharter-0.2.0/apexcharter/inst/examples/input |only apexcharter-0.2.0/apexcharter/inst/examples/proxy |only apexcharter-0.2.0/apexcharter/inst/examples/spark |only apexcharter-0.2.0/apexcharter/inst/examples/sync |only apexcharter-0.2.0/apexcharter/inst/htmlwidgets/apexcharter.css | 65 + apexcharter-0.2.0/apexcharter/inst/htmlwidgets/apexcharter.js | 24 apexcharter-0.2.0/apexcharter/inst/htmlwidgets/apexcharter.yaml | 6 apexcharter-0.2.0/apexcharter/inst/htmlwidgets/assets |only apexcharter-0.2.0/apexcharter/man/apex-facets.Rd |only apexcharter-0.2.0/apexcharter/man/apex.Rd | 8 apexcharter-0.2.0/apexcharter/man/apex_grid.Rd |only apexcharter-0.2.0/apexcharter/man/apexcharter-exports.Rd | 2 apexcharter-0.2.0/apexcharter/man/apexcharter-shiny-facets.Rd |only apexcharter-0.2.0/apexcharter/man/apexcharter-shiny-grid.Rd |only apexcharter-0.2.0/apexcharter/man/ax_chart.Rd | 18 apexcharter-0.2.0/apexcharter/man/ax_colors.Rd | 10 apexcharter-0.2.0/apexcharter/man/ax_dataLabels.Rd | 5 apexcharter-0.2.0/apexcharter/man/ax_fill.Rd | 5 apexcharter-0.2.0/apexcharter/man/ax_grid.Rd | 9 apexcharter-0.2.0/apexcharter/man/ax_legend.Rd | 9 apexcharter-0.2.0/apexcharter/man/ax_plotOptions.Rd | 9 apexcharter-0.2.0/apexcharter/man/ax_proxy_options.Rd | 142 ++-- apexcharter-0.2.0/apexcharter/man/ax_proxy_series.Rd | 158 ++-- apexcharter-0.2.0/apexcharter/man/ax_responsive.Rd | 5 apexcharter-0.2.0/apexcharter/man/ax_states.Rd | 5 apexcharter-0.2.0/apexcharter/man/ax_theme.Rd | 13 apexcharter-0.2.0/apexcharter/man/ax_tooltip.Rd | 9 apexcharter-0.2.0/apexcharter/man/ax_xaxis.Rd | 13 apexcharter-0.2.0/apexcharter/man/ax_yaxis2.Rd | 5 apexcharter-0.2.0/apexcharter/man/bar_opts.Rd | 3 apexcharter-0.2.0/apexcharter/man/consumption.Rd | 2 apexcharter-0.2.0/apexcharter/man/pie_opts.Rd | 4 apexcharter-0.2.0/apexcharter/tests/testthat/test-annotations.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-apex-utils.R | 13 apexcharter-0.2.0/apexcharter/tests/testthat/test-apex.R | 44 + apexcharter-0.2.0/apexcharter/tests/testthat/test-colors.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-facets.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-format.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-grid.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-mixed-charts.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-parse-data.R | 4 apexcharter-0.2.0/apexcharter/tests/testthat/test-proxy.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-spark_box.R |only apexcharter-0.2.0/apexcharter/tests/testthat/test-tooltip.R |only apexcharter-0.2.0/apexcharter/vignettes/apexcharter.Rmd | 38 - apexcharter-0.2.0/apexcharter/vignettes/chart-options.Rmd | 26 apexcharter-0.2.0/apexcharter/vignettes/facets.Rmd |only apexcharter-0.2.0/apexcharter/vignettes/shiny-integration.Rmd | 4 apexcharter-0.2.0/apexcharter/vignettes/spark-box.Rmd | 1 apexcharter-0.2.0/apexcharter/vignettes/sync-charts.Rmd | 25 100 files changed, 1338 insertions(+), 1167 deletions(-)
Title: Bindings to the 'HarfBuzz' and 'Fribidi' Libraries for Text
Shaping
Description: Provides access to the text shaping functionality in the 'HarfBuzz'
library and the bidirectional algorithm in the 'Fribidi' library.
'textshaping' is a low-level utility package mainly for graphic devices that
expands upon the font tool-set provided by the 'systemfonts' package.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between textshaping versions 0.3.3 dated 2021-03-16 and 0.3.4 dated 2021-05-11
DESCRIPTION | 7 +++---- MD5 | 9 +++++---- NEWS.md | 5 +++++ src/Makevars.ucrt |only src/Makevars.win | 2 +- src/utils.h | 30 +++++++++++++++--------------- 6 files changed, 29 insertions(+), 24 deletions(-)
Title: System Native Font Finding
Description: Provides system native access to the font catalogue. As font
handling varies between systems it is difficult to correctly locate
installed fonts across different operating systems. The 'systemfonts'
package provides bindings to the native libraries on Windows, macOS and
Linux for finding font files that can then be used further by e.g. graphic
devices. The main use is intended to be from compiled code but 'systemfonts'
also provides access from R.
Author: Thomas Lin Pedersen [aut, cre]
(<https://orcid.org/0000-0002-5147-4711>),
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
Devon Govett [aut] (Author of font-manager),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between systemfonts versions 1.0.1 dated 2021-02-09 and 1.0.2 dated 2021-05-11
DESCRIPTION | 7 +++---- MD5 | 13 +++++++------ NEWS.md | 5 +++++ inst/doc/c_interface.html | 9 ++++++++- src/Makevars.ucrt |only src/Makevars.win | 2 +- src/font_matching.cpp | 1 + src/ft_cache.cpp | 4 ++-- 8 files changed, 27 insertions(+), 14 deletions(-)
Title: Several Methods for Procedural Name Generation
Description: A small, dependency-free way to generate random names. Methods
provided include the adjective-surname approach of Docker containers
('<https://github.com/moby/moby/blob/master/pkg/namesgenerator/names-generator.go'),
and combinations of common English or Spanish words.
Author: Michael Mahoney [aut, cre] (<https://orcid.org/0000-0003-2402-304X>)
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between proceduralnames versions 0.1.1 dated 2021-01-07 and 0.1.2 dated 2021-05-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ README.md | 18 ++++++++++++------ 4 files changed, 23 insertions(+), 13 deletions(-)
More information about proceduralnames at CRAN
Permanent link
Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>),
Marcel Ramos [ctb, cre] (<https://orcid.org/0000-0002-3242-0582>)
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
Diff between BiocManager versions 1.30.14 dated 2021-05-10 and 1.30.15 dated 2021-05-11
DESCRIPTION | 6 MD5 | 20 NEWS | 9 R/available.R | 9 R/utilities.R | 10 R/valid.R | 4 build/vignette.rds |binary inst/doc/BiocManager.html | 944 +++++++++++++++++++------------------ man/available.Rd | 9 man/valid.Rd | 4 tests/testthat/test_repositories.R | 1 11 files changed, 546 insertions(+), 470 deletions(-)
Title: Spatial Analysis of Field Trials with Splines
Description: Analysis of field trial experiments by modelling spatial trends using two-dimensional Penalised spline (P-spline) models.
Author: Maria Xose Rodriguez-Alvarez [aut, cre],
Martin Boer [aut],
Paul Eilers [aut],
Fred van Eeuwijk [ctb]
Maintainer: Maria Xose Rodriguez-Alvarez <mxrodriguez@bcamath.org>
Diff between SpATS versions 1.0-12 dated 2021-02-26 and 1.0-13 dated 2021-05-11
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS | 3 +++ R/PSANOVA.R | 11 ++++++----- R/SAP.R | 3 ++- R/SpATS.R | 5 +++-- R/construct.2d.pspline.R | 18 ++++++++++++++++-- R/construct.design.matrix.R | 4 ++-- R/construct.spatial.prediction.matrix.R | 5 +++++ R/obtain.spatialtrend.R | 26 +++++++++++++++++++++----- man/PSANOVA.Rd | 4 +++- man/SAP.Rd | 3 ++- man/SpATS-package.Rd | 4 ++-- 13 files changed, 81 insertions(+), 37 deletions(-)
Title: Shiny Matrix Input Field
Description: Implements a custom matrix input field.
Author: Andreas Neudecker
Maintainer: Andreas Neudecker <andreas.neudecker@inwt-statistics.de>
Diff between shinyMatrix versions 0.4.0 dated 2020-10-05 and 0.5.0 dated 2021-05-11
shinyMatrix-0.4.0/shinyMatrix/inst/appCopy |only shinyMatrix-0.4.0/shinyMatrix/inst/appCustom |only shinyMatrix-0.4.0/shinyMatrix/inst/appModal |only shinyMatrix-0.4.0/shinyMatrix/inst/www/matrixInput.css |only shinyMatrix-0.4.0/shinyMatrix/inst/www/matrixInput.js |only shinyMatrix-0.5.0/shinyMatrix/DESCRIPTION | 9 +- shinyMatrix-0.5.0/shinyMatrix/MD5 | 37 ++++----- shinyMatrix-0.5.0/shinyMatrix/NAMESPACE | 1 shinyMatrix-0.5.0/shinyMatrix/R/00-Namespace.R | 2 shinyMatrix-0.5.0/shinyMatrix/R/jsonToMatrix.R | 8 +- shinyMatrix-0.5.0/shinyMatrix/R/matrixInput.R | 64 +++++++++++----- shinyMatrix-0.5.0/shinyMatrix/README.md | 37 +++------ shinyMatrix-0.5.0/shinyMatrix/inst/app/ui.R | 4 - shinyMatrix-0.5.0/shinyMatrix/inst/appDelete |only shinyMatrix-0.5.0/shinyMatrix/inst/appDoubleHeader |only shinyMatrix-0.5.0/shinyMatrix/inst/appExtend/ui.R | 10 +- shinyMatrix-0.5.0/shinyMatrix/inst/appUpdate/server.R | 5 + shinyMatrix-0.5.0/shinyMatrix/inst/www/lodash.min.js |only shinyMatrix-0.5.0/shinyMatrix/inst/www/matrix-input.css |only shinyMatrix-0.5.0/shinyMatrix/inst/www/matrix-input.js |only shinyMatrix-0.5.0/shinyMatrix/inst/www/vue.js |only shinyMatrix-0.5.0/shinyMatrix/man/matrixInput.Rd | 15 ++- 22 files changed, 108 insertions(+), 84 deletions(-)
Title: Simulation of High-Dimensional Data and Parallelized Repeated
Penalized Regression
Description: Simulation of continuous, correlated high-dimensional data with
time to event or binary response, and parallelized functions for Lasso,
Ridge, and Elastic Net penalized regression with repeated starts and
two-dimensional tuning of the Elastic Net.
Author: Levi Waldron <lwaldron.research@gmail.com>
Maintainer: Levi Waldron <lwaldron.research@gmail.com>
Diff between pensim versions 1.3.2 dated 2020-04-20 and 1.3.3 dated 2021-05-11
pensim-1.3.2/pensim/NEWS.md |only pensim-1.3.3/pensim/DESCRIPTION | 8 pensim-1.3.3/pensim/MD5 | 7 pensim-1.3.3/pensim/README.md | 10 pensim-1.3.3/pensim/inst/doc/pensim.html | 435 +++++++++---------------------- 5 files changed, 142 insertions(+), 318 deletions(-)
Title: Visualization of a Correlation Matrix
Description: A graphical display of a correlation matrix or general matrix.
It also contains some algorithms to do matrix reordering. In addition,
corrplot is good at details, including choosing color, text labels,
color labels, layout, etc.
Author: Taiyun Wei [cre, aut],
Viliam Simko [aut],
Michael Levy [ctb],
Yihui Xie [ctb],
Yan Jin [ctb],
Jeff Zemla [ctb],
Moritz Freidank [ctb],
Jun Cai [ctb],
Tomas Protivinsky [ctb]
Maintainer: Taiyun Wei <weitaiyun@gmail.com>
Diff between corrplot versions 0.87 dated 2021-05-08 and 0.88 dated 2021-05-11
DESCRIPTION | 10 MD5 | 36 - R/corrMatOrder.R | 4 R/corrplot.R | 142 ++--- build/vignette.rds |binary inst/NEWS | 15 inst/doc/corrplot-intro.R | 119 +--- inst/doc/corrplot-intro.Rmd | 212 +++----- inst/doc/corrplot-intro.html | 911 +++++++++++++++--------------------- man/corrMatOrder.Rd | 8 man/corrRect.Rd | 14 man/corrRect.hclust.Rd | 14 man/corrplot.Rd | 50 + tests/testthat/test-corrplot.R | 6 vignettes/corrplot-intro.Rmd | 212 +++----- vignettes/example-corrMatOrder.R | 4 vignettes/example-corrRect.R | 14 vignettes/example-corrRect.hclust.R | 14 vignettes/example-corrplot.R | 32 + 19 files changed, 854 insertions(+), 963 deletions(-)
Title: Classical Age-Depth Modelling of Cores from Deposits
Description: Performs 'classical' age-depth modelling of dated sediment deposits - prior to applying more sophisticated techniques such as Bayesian age-depth modelling. Any radiocarbon dated depths are calibrated. Age-depth models are constructed by sampling repeatedly from the dated levels, each time drawing age-depth curves. Model types include linear interpolation, linear or polynomial regression, and a range of splines. See Blaauw (2010). <doi:10.1016/j.quageo.2010.01.002>.
Author: Maarten Blaauw [aut, cre],
J. Andres Christen [ctb],
Judith Esquivel Vazquez [ctb],
Simon Goring [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between clam versions 2.3.8 dated 2021-01-23 and 2.3.9 dated 2021-05-11
clam-2.3.8/clam/man/mix.calibrationcurves.Rd |only clam-2.3.9/clam/DESCRIPTION | 11 ++++--- clam-2.3.9/clam/MD5 | 15 ++++------ clam-2.3.9/clam/NAMESPACE | 6 ---- clam-2.3.9/clam/NEWS.md | 3 ++ clam-2.3.9/clam/R/calibrate.R | 39 --------------------------- clam-2.3.9/clam/R/clam.R | 5 +-- clam-2.3.9/clam/R/readwrite.R | 2 - clam-2.3.9/clam/build/partial.rdb |binary 9 files changed, 20 insertions(+), 61 deletions(-)
Title: Bayesian Estimation for Finite Mixture of Distributions
Description: Provides statistical tools for Bayesian estimation of mixture distributions, mainly a mixture of Gamma, Normal, and t-distributions. The package is implemented based on the Bayesian literature for the finite mixture of distributions, including Mohammadi and et al. (2013) <doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) <doi:10.1080/03610918.2011.588358>.
Author: Reza Mohammadi [aut, cre] (<https://orcid.org/0000-0001-9538-0648>)
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between bmixture versions 1.6 dated 2020-05-26 and 1.7 dated 2021-05-11
DESCRIPTION | 8 ++--- MD5 | 49 +++++++++++++++++----------------- NEWS.md | 8 ++++- R/bmixgamma.R | 63 +++++++++++++++++++++++--------------------- R/bmixnorm.R | 66 ++++++++++++++++++++++++----------------------- R/bmixnorm_bdmcmc.R | 49 +++++++++++++++++----------------- R/bmixt.R | 64 ++++++++++++++++++++++++--------------------- R/mixgamma.R | 35 ++++++++++++------------ R/mixnorm.R | 35 ++++++++++++------------ R/mixt.R | 37 ++++++++++++++------------ R/rdirichlet.R | 30 +++++++++++---------- README.md | 14 +++++---- build |only man/bmixgamma.Rd | 66 ++++++++++++++++++++++++++--------------------- man/bmixnorm.Rd | 58 ++++++++++++++++++++++------------------- man/bmixt.Rd | 63 ++++++++++++++++++++++++-------------------- man/bmixture-internal.Rd | 1 man/bmixture-package.Rd | 12 ++++---- man/galaxy.Rd | 60 +++++++++++++++++++++--------------------- man/mixgamma.Rd | 18 ++++++------ man/mixnorm.Rd | 19 +++++++------ man/mixt.Rd | 26 ++++++++++-------- man/print.bmixt.Rd | 3 +- man/rdirichlet.Rd | 6 ++-- man/summary.bmixnorm.Rd | 1 man/summary.bmixt.Rd | 1 26 files changed, 423 insertions(+), 369 deletions(-)
Title: Native R Kernel for the 'Jupyter Notebook'
Description: The R kernel for the 'Jupyter' environment executes R code which the front-end
('Jupyter Notebook' or other front-ends) submits to the kernel via the network.
Author: Thomas Kluyver [aut, cph],
Philipp Angerer [aut, cph, cre]
(<https://orcid.org/0000-0002-0369-2888>),
Jan Schulz [aut, cph],
Karthik Ram [aut, cph]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>
Diff between IRkernel versions 1.1.1 dated 2020-07-20 and 1.2 dated 2021-05-11
DESCRIPTION | 7 +-- MD5 | 20 ++++++---- R/completion.r | 2 - R/environment_shadow.r | 10 +++-- R/execution.r | 2 - R/kernel.r | 12 ++++-- README.md | 11 +++-- tests/testthat/__pycache__/test_ir.cpython-38.pyc |binary tests/testthat/__pycache__/test_ir.cpython-39.pyc |only tests/testthat/jkt/jupyter_kernel_test/__pycache__/__init__.cpython-39.pyc |only tests/testthat/jkt/jupyter_kernel_test/__pycache__/messagespec.cpython-39.pyc |only tests/testthat/jkt/jupyter_kernel_test/__pycache__/messagespec_common.cpython-39.pyc |only tests/testthat/test_ir.py | 3 + 13 files changed, 39 insertions(+), 28 deletions(-)
Title: Textual Statistics for the Quantitative Analysis of Textual Data
Description: Textual statistics functions formerly in the 'quanteda' package.
Textual statistics for characterizing and comparing textual data. Includes
functions for measuring term and document frequency, the co-occurrence of
words, similarity and distance between features and documents, feature entropy,
keyword occurrence, readability, and lexical diversity. These functions
extend the 'quanteda' package and are specially designed for sparse textual data.
Author: Kenneth Benoit [cre, aut, cph]
(<https://orcid.org/0000-0002-0797-564X>),
Kohei Watanabe [aut] (<https://orcid.org/0000-0001-6519-5265>),
Haiyan Wang [aut] (<https://orcid.org/0000-0003-4992-4311>),
Jiong Wei Lua [aut],
Jouni Kuha [aut] (<https://orcid.org/0000-0002-1156-8465>),
European Research Council [fnd] (ERC-2011-StG 283794-QUANTESS)
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda.textstats versions 0.94 dated 2021-04-06 and 0.94.1 dated 2021-05-11
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/textstat_simil.R | 17 +++++++++-------- R/textstat_summary.R | 15 ++++++++++++--- README.md | 2 +- build/partial.rdb |binary inst/WORDLIST | 1 + tests/testthat/test-textstat_proxy.R | 11 +++-------- 10 files changed, 44 insertions(+), 32 deletions(-)
More information about quanteda.textstats at CRAN
Permanent link
Title: Mail Merge Using R Markdown Documents and 'gmailr'
Description: Mail merge using markdown documents and gmail. With
this package you can parse markdown documents as the body of email,
and the 'yaml' header to specify the subject line of the email. Any
'{}' braces in the email will be encoded with 'glue::glue()'. You can
preview the email in the RStudio viewer pane, and send (draft) email
using 'gmailr'.
Author: Andrie de Vries [aut, cre]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between mailmerge versions 0.2.0 dated 2021-04-12 and 0.2.1 dated 2021-05-11
mailmerge-0.2.0/mailmerge/tests/testthat/test-mm_send_mail.R |only mailmerge-0.2.1/mailmerge/DESCRIPTION | 13 +- mailmerge-0.2.1/mailmerge/MD5 | 24 ++-- mailmerge-0.2.1/mailmerge/NEWS.md | 4 mailmerge-0.2.1/mailmerge/R/helpers.R | 60 +++++------ mailmerge-0.2.1/mailmerge/R/mail_merge.R | 33 ++++-- mailmerge-0.2.1/mailmerge/README.md | 14 ++ mailmerge-0.2.1/mailmerge/inst/WORDLIST | 3 mailmerge-0.2.1/mailmerge/inst/doc/introduction.R | 6 + mailmerge-0.2.1/mailmerge/inst/doc/introduction.html | 8 + mailmerge-0.2.1/mailmerge/man/fragments/intro_example.Rmd | 6 + mailmerge-0.2.1/mailmerge/man/mail_merge.Rd | 5 mailmerge-0.2.1/mailmerge/man/mailmerge-package.Rd | 1 mailmerge-0.2.1/mailmerge/tests/testthat/test-mail_merge.R |only 14 files changed, 119 insertions(+), 58 deletions(-)
Title: Mini Charts for Interactive Maps
Description: Add and modify small charts on an interactive map created with
package 'leaflet'. These charts can be used to represent at same time multiple
variables on a single map.
Author: Veronique Bachelier [aut, cre],
Jalal-Edine ZAWAM [aut],
Benoit Thieurmel [aut],
Francois Guillem [aut],
RTE [cph]
Maintainer: Veronique Bachelier <veronique.bachelier@rte-france.com>
Diff between leaflet.minicharts versions 0.6.0 dated 2019-11-27 and 0.6.2 dated 2021-05-11
DESCRIPTION | 8 MD5 | 36 NAMESPACE | 2 NEWS | 164 - R/add_flows.R | 18 R/add_minicharts.R | 21 R/data-doc.R | 2 README.md | 12 build/vignette.rds |binary inst/doc/introduction.Rmd | 368 +-- inst/doc/introduction.html | 4366 +---------------------------------------- inst/leaflet.minicharts.min.js | 30 man/addFlows.Rd | 269 +- man/addMinicharts.Rd | 438 ++-- man/d3.schemeCategory10.Rd | 44 man/eco2mix.Rd | 70 man/popupArgs.Rd | 92 man/syncWith.Rd | 92 vignettes/introduction.Rmd | 368 +-- 19 files changed, 1199 insertions(+), 5201 deletions(-)
More information about leaflet.minicharts at CRAN
Permanent link
Title: Dynamic Range Boxes
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>,
Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>,
Robert R. Junker <Robert.Junker@sbg.ac.at>,
Jonas Kuppler <Jonas.Kuppler@uni-duesseldorf.de>,
Arne Bathke <Arne.Bathke@sbg.ac.at>,
Judith H. Parkinson <judith.parkinson@sbg.ac.at>,
Raoul Kutil <Raoul_Hugo.Kutil@stud.sbg.ac.at>
Maintainer: Florian Griessenberger <florian.griessenberger@sbg.ac.at>
Diff between dynRB versions 0.15 dated 2018-12-18 and 0.16 dated 2021-05-11
DESCRIPTION | 10 MD5 | 24 - build/vignette.rds |binary inst/doc/TutorialdynRB.R | 18 + inst/doc/TutorialdynRB.html | 633 +++++++++++++++++++++++++++++++------------- man/dynRB-package.Rd | 7 man/dynRB_Pn.Rd | 8 man/dynRB_VPa.Rd | 8 man/dynRB_Vn.Rd | 8 man/finch.Rd | 4 man/finch2.Rd | 4 man/overview.Rd | 8 man/ranks_OV.Rd | 4 13 files changed, 504 insertions(+), 232 deletions(-)
Title: Chaos Game
Description: The main objective of the package is to enter a word of at least two letters based on which an Iterated Function System with Probabilities is constructed, and a two-dimensional fractal containing the chosen word infinitely often is generated via the Chaos Game. Additionally, the package allows to project the two-dimensional fractal on several three-dimensional surfaces and to transform the fractal into another fractal with uniform marginals.
Author: Florian Griessenberger [aut, cre],
Manuela Schreyer [aut],
Johannes Bartel [aut],
Wolfgang Trutschnig [aut]
Maintainer: Florian Griessenberger <florian.griessenberger@sbg.ac.at>
Diff between ChaosGame versions 1.0 dated 2021-03-01 and 1.1 dated 2021-05-11
DESCRIPTION | 11 +++++------ MD5 | 4 ++-- NAMESPACE | 8 +++++++- 3 files changed, 14 insertions(+), 9 deletions(-)
Title: Computes Proximity in Large Sparse Matrices
Description: Computes proximity between rows or columns of large matrices efficiently in C++.
Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries.
Among several built-in similarity/distance measures, computation of correlation,
cosine similarity and Euclidean distance is particularly fast.
Author: Kohei Watanabe [cre, aut, cph]
(<https://orcid.org/0000-0001-6519-5265>),
Robrecht Cannoodt [aut] (<https://orcid.org/0000-0003-3641-729X>)
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between proxyC versions 0.1.5 dated 2019-07-21 and 0.2.0 dated 2021-05-11
DESCRIPTION | 20 +++--- MD5 | 24 +++---- NEWS.md | 40 ++++++++---- R/RcppExports.R | 4 - R/proxy.R | 50 +++++++++------ man/colSds.Rd | 4 - man/simil.Rd | 48 +++++++++++--- src/RcppExports.cpp | 10 +-- src/linear.cpp | 7 +- src/pair.cpp | 142 ++++++++++++++++++++++++++------------------ tests/testthat/test-dist.R | 88 ++++++++++++++++++++------- tests/testthat/test-proxy.R | 95 +++++++++++++++++++---------- tests/testthat/test-simil.R | 23 +++---- 13 files changed, 357 insertions(+), 198 deletions(-)
Title: Relational Data Models
Description: Provides tools for working with multiple related
tables, stored as data frames or in a relational database. Multiple
tables (data and metadata) are stored in a compound object, which can
then be manipulated with a pipe-friendly syntax.
Author: Tobias Schieferdecker [aut],
Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Darko Bergant [aut],
Katharina Brunner [ctb],
James Wondrasek [ctb],
energie360° AG [fnd],
cynkra GmbH [fnd, cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between dm versions 0.2.0 dated 2021-05-03 and 0.2.1 dated 2021-05-11
dm-0.2.0/dm/man/dm_get_fk.Rd |only dm-0.2.1/dm/DESCRIPTION | 16 dm-0.2.1/dm/MD5 | 271 +++--- dm-0.2.1/dm/NAMESPACE | 14 dm-0.2.1/dm/NEWS.md | 25 dm-0.2.1/dm/R/aaa-dbplyr.R | 2 dm-0.2.1/dm/R/aaa-dplyr.R | 2 dm-0.2.1/dm/R/add-tbl.R | 24 dm-0.2.1/dm/R/bind.R | 2 dm-0.2.1/dm/R/data-model-helpers.R | 3 dm-0.2.1/dm/R/datamodelr-code.R | 5 dm-0.2.1/dm/R/db-helpers.R | 49 - dm-0.2.1/dm/R/db-interface.R | 3 dm-0.2.1/dm/R/disambiguate.R | 52 - dm-0.2.1/dm/R/dm-from-src.R | 1 dm-0.2.1/dm/R/dm.R | 209 +---- dm-0.2.1/dm/R/dplyr-src.R | 2 dm-0.2.1/dm/R/dplyr.R | 64 - dm-0.2.1/dm/R/draw-dm.R | 34 dm-0.2.1/dm/R/error-helpers.R | 17 dm-0.2.1/dm/R/examine-constraints.R | 14 dm-0.2.1/dm/R/filter-dm.R | 16 dm-0.2.1/dm/R/filter-helpers.R | 17 dm-0.2.1/dm/R/flatten.R | 6 dm-0.2.1/dm/R/foreign-keys.R | 406 ++++++---- dm-0.2.1/dm/R/global.R | 6 dm-0.2.1/dm/R/graph.R | 2 dm-0.2.1/dm/R/import.R | 5 dm-0.2.1/dm/R/keys.R | 2 dm-0.2.1/dm/R/learn.R | 26 dm-0.2.1/dm/R/nest.R | 9 dm-0.2.1/dm/R/nycflights13.R | 25 dm-0.2.1/dm/R/paste.R | 26 dm-0.2.1/dm/R/pkgdown.R | 4 dm-0.2.1/dm/R/primary-keys.R | 242 +++-- dm-0.2.1/dm/R/ptype.R | 2 dm-0.2.1/dm/R/rows-db.R | 9 dm-0.2.1/dm/R/select-tbl.R | 7 dm-0.2.1/dm/R/select.R | 6 dm-0.2.1/dm/R/table-surgery.R | 6 dm-0.2.1/dm/R/test-dm.R | 68 - dm-0.2.1/dm/R/tidyr.R | 8 dm-0.2.1/dm/R/tidyselect.R | 9 dm-0.2.1/dm/R/unnest.R |only dm-0.2.1/dm/R/upgrade.R |only dm-0.2.1/dm/R/utils.R | 4 dm-0.2.1/dm/R/validate.R |only dm-0.2.1/dm/R/zoom.R | 196 ++-- dm-0.2.1/dm/R/zzx-deprecated.R | 56 - dm-0.2.1/dm/R/zzz.R | 17 dm-0.2.1/dm/demo/berlin.R | 3 dm-0.2.1/dm/demo/nyc.R | 6 dm-0.2.1/dm/demo/seattle.R | 6 dm-0.2.1/dm/inst/doc/dm.html | 10 dm-0.2.1/dm/inst/doc/howto-dm-copy.R | 5 dm-0.2.1/dm/inst/doc/howto-dm-copy.Rmd | 7 dm-0.2.1/dm/inst/doc/howto-dm-copy.html | 18 dm-0.2.1/dm/inst/doc/howto-dm-db.html | 4 dm-0.2.1/dm/inst/doc/howto-dm-df.html | 4 dm-0.2.1/dm/inst/doc/howto-dm-rows.html | 4 dm-0.2.1/dm/inst/doc/howto-dm-theory.html | 38 dm-0.2.1/dm/inst/doc/tech-dm-cdm.html | 71 - dm-0.2.1/dm/inst/doc/tech-dm-class.R | 18 dm-0.2.1/dm/inst/doc/tech-dm-class.Rmd | 67 - dm-0.2.1/dm/inst/doc/tech-dm-class.html | 122 +-- dm-0.2.1/dm/inst/doc/tech-dm-draw.html | 4 dm-0.2.1/dm/inst/doc/tech-dm-filter.R | 3 dm-0.2.1/dm/inst/doc/tech-dm-filter.Rmd | 3 dm-0.2.1/dm/inst/doc/tech-dm-filter.html | 118 +- dm-0.2.1/dm/inst/doc/tech-dm-join.R | 3 dm-0.2.1/dm/inst/doc/tech-dm-join.Rmd | 3 dm-0.2.1/dm/inst/doc/tech-dm-join.html | 47 - dm-0.2.1/dm/inst/doc/tech-dm-low-level.html | 4 dm-0.2.1/dm/inst/doc/tech-dm-zoom.html | 68 - dm-0.2.1/dm/inst/extdata |only dm-0.2.1/dm/man/dm.Rd | 16 dm-0.2.1/dm/man/dm_add_fk.Rd | 89 -- dm-0.2.1/dm/man/dm_add_pk.Rd | 47 - dm-0.2.1/dm/man/dm_enum_fk_candidates.Rd | 3 dm-0.2.1/dm/man/dm_get_all_fks.Rd | 22 dm-0.2.1/dm/man/dm_get_all_pks.Rd | 18 dm-0.2.1/dm/man/dm_get_pk.Rd | 48 - dm-0.2.1/dm/man/dm_has_fk.Rd | 31 dm-0.2.1/dm/man/dm_has_pk.Rd | 2 dm-0.2.1/dm/man/dm_rm_fk.Rd |only dm-0.2.1/dm/man/dm_rm_pk.Rd |only dm-0.2.1/dm/man/dplyr_src.Rd | 2 dm-0.2.1/dm/man/enum_pk_candidates.Rd | 4 dm-0.2.1/dm/tests/testthat/_snaps/bind.md | 44 - dm-0.2.1/dm/tests/testthat/_snaps/dm.md | 34 dm-0.2.1/dm/tests/testthat/_snaps/dplyr.md | 389 +++++++++ dm-0.2.1/dm/tests/testthat/_snaps/draw-dm.md | 105 ++ dm-0.2.1/dm/tests/testthat/_snaps/draw-dm/dm-for-filter.svg |only dm-0.2.1/dm/tests/testthat/_snaps/draw-dm/nycflight-dm-copy.svg | 4 dm-0.2.1/dm/tests/testthat/_snaps/error-helpers.md | 11 dm-0.2.1/dm/tests/testthat/_snaps/examine-constraints.md | 8 dm-0.2.1/dm/tests/testthat/_snaps/filter-dm.md | 208 +++++ dm-0.2.1/dm/tests/testthat/_snaps/foreign-keys.md | 210 ++++- dm-0.2.1/dm/tests/testthat/_snaps/paste.md | 48 - dm-0.2.1/dm/tests/testthat/_snaps/primary-keys.md | 177 ++++ dm-0.2.1/dm/tests/testthat/_snaps/rows-dm.md | 348 ++++---- dm-0.2.1/dm/tests/testthat/_snaps/select-tbl.md | 4 dm-0.2.1/dm/tests/testthat/_snaps/select.md | 57 + dm-0.2.1/dm/tests/testthat/_snaps/tidyr.md | 196 ++++ dm-0.2.1/dm/tests/testthat/_snaps/zoom.md | 74 + dm-0.2.1/dm/tests/testthat/_snaps/zzx-deprecated.md |only dm-0.2.1/dm/tests/testthat/dm |only dm-0.2.1/dm/tests/testthat/helper-expectations.R | 15 dm-0.2.1/dm/tests/testthat/helper-print.R | 6 dm-0.2.1/dm/tests/testthat/helper-src.R | 140 +-- dm-0.2.1/dm/tests/testthat/helper-zoom.R | 16 dm-0.2.1/dm/tests/testthat/setup.R |only dm-0.2.1/dm/tests/testthat/test-db-interface.R | 7 dm-0.2.1/dm/tests/testthat/test-disambiguate.R | 4 dm-0.2.1/dm/tests/testthat/test-dm-from-src.R | 9 dm-0.2.1/dm/tests/testthat/test-dm.R | 223 ----- dm-0.2.1/dm/tests/testthat/test-dplyr-src.R |only dm-0.2.1/dm/tests/testthat/test-dplyr.R | 276 +++--- dm-0.2.1/dm/tests/testthat/test-draw-dm.R | 71 - dm-0.2.1/dm/tests/testthat/test-error-helpers.R | 4 dm-0.2.1/dm/tests/testthat/test-filter-dm.R | 53 - dm-0.2.1/dm/tests/testthat/test-flatten.R | 21 dm-0.2.1/dm/tests/testthat/test-foreign-keys.R | 158 ++- dm-0.2.1/dm/tests/testthat/test-learn.R | 66 - dm-0.2.1/dm/tests/testthat/test-nest.R | 12 dm-0.2.1/dm/tests/testthat/test-paste.R | 5 dm-0.2.1/dm/tests/testthat/test-primary-keys.R | 98 +- dm-0.2.1/dm/tests/testthat/test-rows-db.R | 2 dm-0.2.1/dm/tests/testthat/test-rows-dm.R | 36 dm-0.2.1/dm/tests/testthat/test-schema.R | 3 dm-0.2.1/dm/tests/testthat/test-select-tbl.R | 3 dm-0.2.1/dm/tests/testthat/test-select.R | 106 +- dm-0.2.1/dm/tests/testthat/test-table-surgery.R | 6 dm-0.2.1/dm/tests/testthat/test-tidyr.R | 57 - dm-0.2.1/dm/tests/testthat/test-upgrade.R |only dm-0.2.1/dm/tests/testthat/test-utils.R | 4 dm-0.2.1/dm/tests/testthat/test-validate.R |only dm-0.2.1/dm/tests/testthat/test-zoom.R | 47 - dm-0.2.1/dm/tests/testthat/test-zzx-deprecated.R | 145 +-- dm-0.2.1/dm/vignettes/howto-dm-copy.Rmd | 7 dm-0.2.1/dm/vignettes/tech-dm-class.Rmd | 67 - dm-0.2.1/dm/vignettes/tech-dm-filter.Rmd | 3 dm-0.2.1/dm/vignettes/tech-dm-join.Rmd | 3 143 files changed, 3836 insertions(+), 2661 deletions(-)
Title: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm
Description: Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm from McCormick et al. (2016) <DOI:10.1080/01621459.2016.1152191>. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA4' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Author: Zehang Richard Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Richard Li <lizehang@gmail.com>
Diff between InSilicoVA versions 1.3.0 dated 2020-06-30 and 1.3.1 dated 2021-05-11
InSilicoVA-1.3.0/InSilicoVA/man/InsilicoVA-package.Rd |only InSilicoVA-1.3.0/InSilicoVA/tests/testthat/warnings.txt |only InSilicoVA-1.3.1/InSilicoVA/DESCRIPTION | 10 +- InSilicoVA-1.3.1/InSilicoVA/MD5 | 56 +++++------ InSilicoVA-1.3.1/InSilicoVA/NEWS.md | 5 - InSilicoVA-1.3.1/InSilicoVA/R/diag.r | 9 + InSilicoVA-1.3.1/InSilicoVA/R/get_indiv.r | 23 ++-- InSilicoVA-1.3.1/InSilicoVA/R/groupplot.r | 9 + InSilicoVA-1.3.1/InSilicoVA/R/indivplot.r | 9 + InSilicoVA-1.3.1/InSilicoVA/R/insilico_core.r | 4 InSilicoVA-1.3.1/InSilicoVA/R/insilico_standard.r | 6 - InSilicoVA-1.3.1/InSilicoVA/R/insilico_train.r | 2 InSilicoVA-1.3.1/InSilicoVA/R/plot.r | 9 + InSilicoVA-1.3.1/InSilicoVA/R/print_insilico.r | 9 + InSilicoVA-1.3.1/InSilicoVA/R/print_insilico_summary.r | 9 + InSilicoVA-1.3.1/InSilicoVA/R/report.r | 9 + InSilicoVA-1.3.1/InSilicoVA/man/csmf.diag.Rd | 19 ++-- InSilicoVA-1.3.1/InSilicoVA/man/extract.prob.Rd | 11 +- InSilicoVA-1.3.1/InSilicoVA/man/get.indiv.Rd | 19 ++-- InSilicoVA-1.3.1/InSilicoVA/man/indivplot.Rd | 31 ++++-- InSilicoVA-1.3.1/InSilicoVA/man/insilico.Rd | 57 ++++++++---- InSilicoVA-1.3.1/InSilicoVA/man/insilico.fit.Rd | 66 ++++++++++---- InSilicoVA-1.3.1/InSilicoVA/man/insilico.train.Rd | 57 ++++++++---- InSilicoVA-1.3.1/InSilicoVA/man/physician_debias.Rd | 12 ++ InSilicoVA-1.3.1/InSilicoVA/man/plot.insilico.Rd | 32 ++++-- InSilicoVA-1.3.1/InSilicoVA/man/print.insilico.Rd | 8 - InSilicoVA-1.3.1/InSilicoVA/man/print.insilico_summary.Rd | 8 - InSilicoVA-1.3.1/InSilicoVA/man/stackplot.Rd | 36 +++++-- InSilicoVA-1.3.1/InSilicoVA/man/summary.insilico.Rd | 19 ++-- InSilicoVA-1.3.1/InSilicoVA/man/updateIndiv.Rd | 8 - 30 files changed, 361 insertions(+), 191 deletions(-)
Title: Functions for Medical Statistics Book with some Demographic Data
Description: Several utility functions for the book entitled
"Practices of Medical and Health Data Analysis using R"
(Pearson Education Japan, 2007) with Japanese demographic
data and some demographic analysis related functions.
Author: Minato Nakazawa <minato-nakazawa@umin.net>
Maintainer: Minato Nakazawa <minato-nakazawa@umin.net>
Diff between fmsb versions 0.7.0 dated 2019-12-15 and 0.7.1 dated 2021-05-11
DESCRIPTION | 8 +++---- MD5 | 37 +++++++++++++++++++----------------- NAMESPACE | 3 +- NEWS | 6 +++++ R/demogjpn.R | 49 ++++++++++++++++++++++++++++-------------------- build |only man/CM.Rd | 4 --- man/CT.Rd | 3 -- man/Denny.Rd | 3 -- man/H27MPJ.Rd |only man/Hadwiger.Rd | 3 -- man/JASM.Rd | 5 ---- man/Jfert.Rd | 7 ++---- man/Jlife.Rd | 10 ++++----- man/Jpop.Rd | 6 ++--- man/Jpopl.Rd | 6 ++--- man/Jvital.Rd | 30 ++++++++++++++--------------- man/Jvital2013byPref.Rd | 4 +-- man/PrefYLL2015.Rd | 8 +++---- man/S60MPJ.Rd | 2 - tests |only 21 files changed, 102 insertions(+), 92 deletions(-)
Title: Biological Structure Analysis
Description: Utilities to process, organize and explore protein structure,
sequence and dynamics data. Features include the ability to read and write
structure, sequence and dynamic trajectory data, perform sequence and structure
database searches, data summaries, atom selection, alignment, superposition,
rigid core identification, clustering, torsion analysis, distance matrix
analysis, structure and sequence conservation analysis, normal mode analysis,
principal component analysis of heterogeneous structure data, and correlation
network analysis from normal mode and molecular dynamics data. In addition,
various utility functions are provided to enable the statistical and graphical
power of the R environment to work with biological sequence and structural data.
Please refer to the URLs below for more information.
Author: Barry Grant [aut, cre],
Xin-Qiu Yao [aut],
Lars Skjaerven [aut],
Julien Ide [aut]
Maintainer: Barry Grant <bjgrant@ucsd.edu>
Diff between bio3d versions 2.4-1 dated 2020-01-21 and 2.4-2 dated 2021-05-11
DESCRIPTION | 13 MD5 | 154 ++++----- NAMESPACE | 6 R/aanma.pdbs.R | 49 -- R/arg_filter.R |only R/blast.pdb.R | 23 + R/chain.pdb.R | 53 ++- R/cmap.pdb.R | 41 ++ R/cna.ensmb.R | 1 R/cnapath.R | 8 R/core.cmap.R | 34 -- R/dm.R | 40 ++ R/filter.dccm.R | 73 ++++ R/get.blast.R | 6 R/get.seq.R | 30 + R/hmmer.R | 17 - R/pb.R |only R/pca.array.R | 22 + R/pdb.annotate.R | 621 ++++++++++++++++++++++++++++--------- R/pdbs2pdb.R | 23 + R/plot.blast.R | 2 R/plot.cna.R | 37 ++ R/plot.dccm.R | 29 + R/pymol.pdbs.R | 33 + R/read.dcd.R | 10 R/summary.cnapath.R | 15 R/vmd.cna.R | 12 R/vmd.cnapath.R | 69 +++- README.md | 39 +- inst/doc/bio3d_vignettes.Rmd | 41 +- inst/doc/bio3d_vignettes.html | 30 - man/aa.index.Rd | 4 man/aa2index.Rd | 2 man/bio3d.package.Rd | 15 man/blast.pdb.Rd | 2 man/chain.pdb.Rd | 2 man/cmap.Rd | 8 man/cna.Rd | 13 man/cnapath.Rd | 17 - man/dm.Rd | 12 man/dssp.Rd | 4 man/filter.dccm.Rd | 12 man/fit.xyz.Rd | 10 man/get.seq.Rd | 2 man/hmmer.Rd | 2 man/identify.cna.Rd | 6 man/layout.cna.Rd | 4 man/mustang.Rd | 2 man/pca.array.Rd | 5 man/pdb.annotate.Rd | 25 - man/pdbs2pdb.Rd | 3 man/plot.cna.Rd | 8 man/print.cna.Rd | 4 man/pymol.Rd | 11 man/read.fasta.Rd | 2 man/read.ncdf.Rd | 6 man/seq2aln.Rd | 2 man/seqaln.Rd | 8 man/seqaln.pair.Rd | 2 man/uniprot.Rd | 2 man/vmd.cna.Rd | 14 man/write.fasta.Rd | 2 man/write.ncdf.Rd | 6 src/read_pdb.cpp | 14 tests/testthat/test-aanma.pdbs.R | 2 tests/testthat/test-clean.pdb.R | 18 - tests/testthat/test-cna.R | 6 tests/testthat/test-fitting.R | 10 tests/testthat/test-get.pdb.R | 8 tests/testthat/test-get.seq.R | 127 ++++++- tests/testthat/test-mol2.R | 12 tests/testthat/test-nma.R | 4 tests/testthat/test-pdb.annotate.R | 50 +- tests/testthat/test-pdbsplit.R | 15 tests/testthat/test-read.all.R | 4 tests/testthat/test-read.cif.R | 10 tests/testthat/test-read.pdb.R | 39 +- tests/testthat/test-seqaln.R | 4 vignettes/bio3d_vignettes.Rmd | 41 +- 79 files changed, 1493 insertions(+), 619 deletions(-)
Title: Simulating Spreading Activation in a Network
Description: The notion of spreading activation is a prevalent metaphor in the cognitive sciences. This package provides the tools for cognitive scientists and psychologists to conduct computer simulations that implement spreading activation in a network representation. The algorithmic method implemented in 'spreadr' subroutines follows the approach described in Vitevitch, Ercal, and Adagarla (2011, Frontiers), who viewed activation as a fixed cognitive resource that could spread among nodes that were connected to each other via edges or connections (i.e., a network). See Vitevitch, M. S., Ercal, G., & Adagarla, B. (2011). Simulating retrieval from a highly clustered network: Implications for spoken word recognition. Frontiers in Psychology, 2, 369. <doi:10.3389/fpsyg.2011.00369> and Siew, C. S. Q. (2019). spreadr: A R package to simulate spreading activation in a network. Behavior Research Methods, 51, 910-929. <doi: 10.3758/s13428-018-1186-5>.
Author: Cynthia Siew [aut, cre],
Dirk U. Wulff [ctb],
Ning Yuan Lee [ctb]
Maintainer: Cynthia Siew <cynsiewsq@gmail.com>
Diff between spreadr versions 0.1.0 dated 2018-11-19 and 0.2.0 dated 2021-05-11
spreadr-0.1.0/spreadr/R/spreadr_2.R |only spreadr-0.1.0/spreadr/R/zzz.R |only spreadr-0.1.0/spreadr/man/spreadr_2.Rd |only spreadr-0.2.0/spreadr/DESCRIPTION | 32 spreadr-0.2.0/spreadr/MD5 | 32 spreadr-0.2.0/spreadr/NAMESPACE | 10 spreadr-0.2.0/spreadr/NEWS.md |only spreadr-0.2.0/spreadr/R/data.R |only spreadr-0.2.0/spreadr/R/spreadr.R | 308 +- spreadr-0.2.0/spreadr/build/vignette.rds |binary spreadr-0.2.0/spreadr/data |only spreadr-0.2.0/spreadr/inst/doc/spreadr_vignette.R | 194 + spreadr-0.2.0/spreadr/inst/doc/spreadr_vignette.Rmd | 333 ++- spreadr-0.2.0/spreadr/inst/doc/spreadr_vignette.html | 2066 ++++++++++++++++--- spreadr-0.2.0/spreadr/man/pnet.Rd |only spreadr-0.2.0/spreadr/man/pnetm.Rd |only spreadr-0.2.0/spreadr/man/spreadr.Rd | 118 - spreadr-0.2.0/spreadr/src/RcppExports.cpp | 4 spreadr-0.2.0/spreadr/src/create_mat_t.cpp | 30 spreadr-0.2.0/spreadr/vignettes/sources.bib |only spreadr-0.2.0/spreadr/vignettes/spreadr_vignette.Rmd | 333 ++- 21 files changed, 2791 insertions(+), 669 deletions(-)
Title: Matching-Adjusted Indirect Comparison
Description: A generalised workflow for generation of subject weights to be
used in Matching-Adjusted Indirect Comparison (MAIC) per Signorovitch et
al (2012) <doi:10.1016/j.jval.2012.05.004>, Signorovitch et al (2010)
<doi:10.2165/11538370-000000000-00000>. In MAIC, unbiased
comparison between outcomes of two trials is facilitated by weighting the
subject-level outcomes of one trial with weights derived such that the
weighted aggregate measures of the prognostic or effect modifying variables
are equal to those of the sample in the comparator trial. The functions and
classes included in this package wrap and abstract the process demonstrated
in the UK National Institute for Health and Care Excellence Decision
Support Unit (NICE DSU)'s example (Phillippo et al, (2016) [see URL]),
providing a repeatable and easily specifiable workflow for producing
multiple comparison variable sets against a variety of target studies, with
preprocessing for a number of aggregate target forms (e.g. mean, median,
domain limits).
Author: Rob Young [aut, cre]
Maintainer: Rob Young <rob.young@heor.co.uk>
Diff between maic versions 0.1.2 dated 2020-04-30 and 0.1.3 dated 2021-05-11
DESCRIPTION | 11 MD5 | 24 NEWS.md | 43 R/examples/maic.example.R | 76 - R/examples/maic.weight.example.R | 58 - R/maic.R | 1799 ++++++++++++++++----------------- README.md | 214 +-- man/createMAICInput.Rd | 8 man/reportCovariates.Rd | 5 tests/testthat.R | 8 tests/testthat/test_maicInput.R | 864 +++++++-------- tests/testthat/test_maicWeighting.R | 599 +++++----- tests/testthat/test_reportCovariates.R | 268 ++-- 13 files changed, 1984 insertions(+), 1993 deletions(-)
Title: Colorblind-Friendly Color Maps for R
Description: Color maps designed to improve graph readability for readers with
common forms of color blindness and/or color vision deficiency. The color
maps are also perceptually-uniform, both in regular form and also when
converted to black-and-white for printing. This package also contains
'ggplot2' bindings for discrete and continuous color and fill scales. A lean
version of the package called 'viridisLite' that does not include the
'ggplot2' bindings can be found at
<https://cran.r-project.org/package=viridisLite>.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph],
Bob Rudis [ctb, cph],
Marco Sciaini [ctb, cph],
Antônio Pedro Camargo [ctb, cph],
Cédric Scherer [ctb, cph]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridis versions 0.6.0 dated 2021-04-15 and 0.6.1 dated 2021-05-11
DESCRIPTION | 9 +++--- MD5 | 16 ++++++---- NEWS.md | 17 ++++++++++- R/scales.R | 20 +++++++++++++ data |only inst/doc/intro-to-viridis.R | 15 +++++----- inst/doc/intro-to-viridis.Rmd | 15 +++++----- inst/doc/intro-to-viridis.html | 61 ++++++++++++++++++++--------------------- man/unemp.Rd |only vignettes/intro-to-viridis.Rmd | 15 +++++----- 10 files changed, 104 insertions(+), 64 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut] (<https://orcid.org/0000-0001-8538-6691>),
Melissa Hallow [aut],
Wenping Wang [aut, cre],
Zufar Mulyukov [ctb],
Alan Hindmarsh [ctb],
Awad H. Al-Mohy [ctb],
Matt Dowle [ctb],
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Arun Srinivasan [ctb],
Ernst Hairer [ctb],
Gerhard Wanner [ctb],
Goro Fuji [ctb],
Hadley Wickham [ctb],
Jack Dongarra [ctb],
Linda Petzold [ctb],
Martin Maechler [ctb],
Matteo Fasiolo [ctb],
Morwenn [ctb],
Nicholas J. Higham [ctb],
Roger B. Sidje [ctb],
Simon Frost [ctb],
Kevin Ushey [ctb],
Yu Feng [ctb]
Maintainer: Wenping Wang <wwang8198@gmail.com>
Diff between RxODE versions 1.0.8 dated 2021-04-10 and 1.0.9 dated 2021-05-11
RxODE-1.0.8/RxODE/inst/tools/r-stripper |only RxODE-1.0.9/RxODE/DESCRIPTION | 10 RxODE-1.0.9/RxODE/MD5 | 72 +++-- RxODE-1.0.9/RxODE/NEWS.md | 31 ++ RxODE-1.0.9/RxODE/R/RxODE_md5.R | 2 RxODE-1.0.9/RxODE/R/rxParams.R | 25 +- RxODE-1.0.9/RxODE/R/rxsolve.R | 73 +++-- RxODE-1.0.9/RxODE/build/partial.rdb |binary RxODE-1.0.9/RxODE/configure | 5 RxODE-1.0.9/RxODE/configure.win | 5 RxODE-1.0.9/RxODE/inst/doc/RxODE-syntax.html | 14 - RxODE-1.0.9/RxODE/inst/include/RxODE.h | 1 RxODE-1.0.9/RxODE/inst/tools/workaround.R |only RxODE-1.0.9/RxODE/inst/workaround.R |only RxODE-1.0.9/RxODE/src/Makevars.in | 2 RxODE-1.0.9/RxODE/src/cfode.c | 46 +-- RxODE-1.0.9/RxODE/src/cfode_static.c | 8 RxODE-1.0.9/RxODE/src/common.h | 2 RxODE-1.0.9/RxODE/src/corfailure.c | 16 - RxODE-1.0.9/RxODE/src/correction.c | 88 +++---- RxODE-1.0.9/RxODE/src/etTran.cpp | 12 RxODE-1.0.9/RxODE/src/intdy.c | 28 +- RxODE-1.0.9/RxODE/src/lsoda.c | 210 ++++++++--------- RxODE-1.0.9/RxODE/src/methodswitch.c | 64 ++--- RxODE-1.0.9/RxODE/src/ode.h | 4 RxODE-1.0.9/RxODE/src/orderswitch.c | 66 ++--- RxODE-1.0.9/RxODE/src/par_solve.cpp | 39 --- RxODE-1.0.9/RxODE/src/prja.c | 36 +- RxODE-1.0.9/RxODE/src/rxData.cpp | 146 ----------- RxODE-1.0.9/RxODE/src/rxData.h | 2 RxODE-1.0.9/RxODE/src/scaleh.c | 36 +- RxODE-1.0.9/RxODE/src/solsy.c | 12 RxODE-1.0.9/RxODE/src/stoda.c | 268 +++++++++++----------- RxODE-1.0.9/RxODE/src/strncmp.c |only RxODE-1.0.9/RxODE/src/strncmp.h |only RxODE-1.0.9/RxODE/tests/testthat/test-idFactor.R | 20 - RxODE-1.0.9/RxODE/tests/testthat/test-issue-410.R |only RxODE-1.0.9/RxODE/tests/testthat/test-pipeline.R | 156 ------------ RxODE-1.0.9/RxODE/tests/testthat/test-resample.R | 26 -- 39 files changed, 609 insertions(+), 916 deletions(-)
Title: Convert Plot to 'grob' or 'ggplot' Object
Description: Convert plot function call (using expression or formula) to 'grob' or 'ggplot' object that compatible to the 'grid' and 'ggplot2' ecosystem. With this package, we are able to e.g. using 'cowplot' to align plots produced by 'base' graphics, 'ComplexHeatmap', 'eulerr', 'grid', 'lattice', 'magick', 'pheatmap', 'vcd' etc. by converting them to 'ggplot' objects.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggplotify versions 0.0.6 dated 2021-04-22 and 0.0.7 dated 2021-05-11
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 4 ++++ R/as-grob.R | 9 +++++++++ inst/doc/ggplotify.html | 8 ++++---- man/as-grob.Rd | 3 +++ 7 files changed, 30 insertions(+), 13 deletions(-)
Title: Fetch 'Phylogenies' from Many Sources
Description: Includes methods for fetching 'phylogenies' from a variety
of sources, including the 'Phylomatic' web service
(<http://phylodiversity.net/phylomatic/>), and 'Phylocom'
(<https://github.com/phylocom/phylocom/>).
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between brranching versions 0.6.0 dated 2020-06-12 and 0.7.0 dated 2021-05-11
brranching-0.6.0/brranching/build |only brranching-0.6.0/brranching/inst/doc |only brranching-0.6.0/brranching/vignettes |only brranching-0.7.0/brranching/DESCRIPTION | 19 ++++------ brranching-0.7.0/brranching/MD5 | 12 ++---- brranching-0.7.0/brranching/NEWS.md | 8 ++++ brranching-0.7.0/brranching/README.md | 9 +--- brranching-0.7.0/brranching/tests/testthat/test-phylomatic_names.R | 15 ++----- 8 files changed, 28 insertions(+), 35 deletions(-)
Title: Interface to Bold Systems API
Description: A programmatic interface to the Web Service methods provided by
Bold Systems (<http://www.boldsystems.org/>) for genetic 'barcode' data.
Functions include methods for searching by sequences by taxonomic names,
ids, collectors, and institutions; as well as a function for searching
for specimens, and downloading trace files.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between bold versions 1.1.0 dated 2020-06-17 and 1.2.0 dated 2021-05-11
bold-1.1.0/bold/build |only bold-1.1.0/bold/inst |only bold-1.1.0/bold/vignettes |only bold-1.2.0/bold/DESCRIPTION | 14 +++++++------- bold-1.2.0/bold/LICENSE | 4 ++-- bold-1.2.0/bold/MD5 | 13 ++++--------- bold-1.2.0/bold/NEWS.md | 7 +++++++ bold-1.2.0/bold/README.md | 8 ++------ 8 files changed, 22 insertions(+), 24 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-07 1.22.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-26 0.2.3.3
Title: Tools for Analysing and Visualising Workplace Analytics Data
Description: Opinionated functions that enable easier and faster
analysis of Workplace Analytics data. There are three main types of functions in 'wpa':
(i) Standard functions create a 'ggplot' visual or a summary table based on a specific
Workplace Analytics metric; (2) Report Generation functions generate HTML reports on
a specific analysis area, e.g. Collaboration; (3) Other miscellaneous functions cover
more specific applications (e.g. Subject Line text mining) of Workplace Analytics data.
This package adheres to 'tidyverse' principles and works well with the pipe syntax.
'wpa' is built with the beginner-to-intermediate R users in mind, and is optimised for
simplicity.
Author: Martin Chan [aut, cre],
Carlos Morales [aut],
Mark Powers [ctb],
Ainize Cidoncha [ctb],
Rosamary Ochoa Vargas [ctb],
Tannaz Sattari [ctb],
Lucas Hogner [ctb],
Jasminder Thind [ctb],
Simone Liebal [ctb],
Ellen Trinklein [ctb],
Microsoft Corporation [cph]
Maintainer: Martin Chan <martin.chan@microsoft.com>
Diff between wpa versions 1.4.3 dated 2021-04-06 and 1.5.0 dated 2021-05-11
wpa-1.4.3/wpa/data/datalist |only wpa-1.5.0/wpa/DESCRIPTION | 6 wpa-1.5.0/wpa/MD5 | 301 ++++++++++++------------- wpa-1.5.0/wpa/NAMESPACE | 1 wpa-1.5.0/wpa/NEWS.md | 11 wpa-1.5.0/wpa/R/IV_by_Period.R | 4 wpa-1.5.0/wpa/R/check_query.R | 75 +++++- wpa-1.5.0/wpa/R/collaboration_rank.R | 2 wpa-1.5.0/wpa/R/create_bar.R | 80 ++---- wpa-1.5.0/wpa/R/create_bar_asis.R | 12 wpa-1.5.0/wpa/R/create_boxplot.R | 4 wpa-1.5.0/wpa/R/create_dist.R | 194 +++++++++++++--- wpa-1.5.0/wpa/R/create_fizz.R | 32 ++ wpa-1.5.0/wpa/R/create_hist.R | 11 wpa-1.5.0/wpa/R/create_line.R | 59 ++-- wpa-1.5.0/wpa/R/create_period_scatter.R | 20 - wpa-1.5.0/wpa/R/create_rank.R | 5 wpa-1.5.0/wpa/R/create_scatter.R | 3 wpa-1.5.0/wpa/R/create_stacked.R | 156 ++++++++++-- wpa-1.5.0/wpa/R/create_trend.R | 21 + wpa-1.5.0/wpa/R/cut_hour.R | 63 ++++- wpa-1.5.0/wpa/R/export.R | 2 wpa-1.5.0/wpa/R/flag_ch_ratio.R | 2 wpa-1.5.0/wpa/R/flex_index.R | 7 wpa-1.5.0/wpa/R/generate_report.R | 2 wpa-1.5.0/wpa/R/globals.R | 10 wpa-1.5.0/wpa/R/hrvar_count_all.R | 5 wpa-1.5.0/wpa/R/hrvar_trend.R |only wpa-1.5.0/wpa/R/identify_nkw.R | 27 +- wpa-1.5.0/wpa/R/init.R | 2 wpa-1.5.0/wpa/R/meetingtype_dist_ca.R | 4 wpa-1.5.0/wpa/R/meetingtype_dist_mt.R | 4 wpa-1.5.0/wpa/R/mgrrel_matrix.R | 50 +--- wpa-1.5.0/wpa/R/network_describe.R | 2 wpa-1.5.0/wpa/R/one2one_freq.R | 106 +++++--- wpa-1.5.0/wpa/R/p_test.R | 2 wpa-1.5.0/wpa/R/period_change.R | 2 wpa-1.5.0/wpa/R/personas_hclust.R | 1 wpa-1.5.0/wpa/R/remove_outliers.R | 2 wpa-1.5.0/wpa/R/tm_cooc.R | 4 wpa-1.5.0/wpa/R/track_hr_change.R | 4 wpa-1.5.0/wpa/R/workpatterns_classify.R | 86 +++++-- wpa-1.5.0/wpa/R/workpatterns_classify_bw.R | 240 ++++++++++++++++++- wpa-1.5.0/wpa/R/workpatterns_classify_pav.R | 2 wpa-1.5.0/wpa/R/workpatterns_rank.R | 11 wpa-1.5.0/wpa/R/workpatterns_report.R | 46 +-- wpa-1.5.0/wpa/README.md | 3 wpa-1.5.0/wpa/build/vignette.rds |binary wpa-1.5.0/wpa/inst/doc/intro-to-wpa.Rmd | 2 wpa-1.5.0/wpa/inst/doc/intro-to-wpa.html | 57 ++-- wpa-1.5.0/wpa/man/IV_by_period.Rd | 5 wpa-1.5.0/wpa/man/afterhours_dist.Rd | 1 wpa-1.5.0/wpa/man/afterhours_fizz.Rd | 1 wpa-1.5.0/wpa/man/afterhours_line.Rd | 1 wpa-1.5.0/wpa/man/afterhours_rank.Rd | 1 wpa-1.5.0/wpa/man/afterhours_summary.Rd | 1 wpa-1.5.0/wpa/man/afterhours_trend.Rd | 4 wpa-1.5.0/wpa/man/check_query.Rd | 4 wpa-1.5.0/wpa/man/collaboration_area.Rd | 1 wpa-1.5.0/wpa/man/collaboration_dist.Rd | 1 wpa-1.5.0/wpa/man/collaboration_fizz.Rd | 1 wpa-1.5.0/wpa/man/collaboration_line.Rd | 1 wpa-1.5.0/wpa/man/collaboration_rank.Rd | 5 wpa-1.5.0/wpa/man/collaboration_sum.Rd | 1 wpa-1.5.0/wpa/man/collaboration_trend.Rd | 4 wpa-1.5.0/wpa/man/create_bar.Rd | 24 + wpa-1.5.0/wpa/man/create_bar_asis.Rd | 1 wpa-1.5.0/wpa/man/create_boxplot.Rd | 1 wpa-1.5.0/wpa/man/create_bubble.Rd | 1 wpa-1.5.0/wpa/man/create_dist.Rd | 40 +++ wpa-1.5.0/wpa/man/create_fizz.Rd | 1 wpa-1.5.0/wpa/man/create_line.Rd | 1 wpa-1.5.0/wpa/man/create_line_asis.Rd | 1 wpa-1.5.0/wpa/man/create_period_scatter.Rd | 1 wpa-1.5.0/wpa/man/create_rank.Rd | 8 wpa-1.5.0/wpa/man/create_sankey.Rd | 1 wpa-1.5.0/wpa/man/create_scatter.Rd | 1 wpa-1.5.0/wpa/man/create_stacked.Rd | 22 + wpa-1.5.0/wpa/man/create_trend.Rd | 10 wpa-1.5.0/wpa/man/cut_hour.Rd | 8 wpa-1.5.0/wpa/man/email_dist.Rd | 1 wpa-1.5.0/wpa/man/email_fizz.Rd | 1 wpa-1.5.0/wpa/man/email_line.Rd | 1 wpa-1.5.0/wpa/man/email_rank.Rd | 1 wpa-1.5.0/wpa/man/email_summary.Rd | 1 wpa-1.5.0/wpa/man/email_trend.Rd | 4 wpa-1.5.0/wpa/man/export.Rd | 3 wpa-1.5.0/wpa/man/external_network_plot.Rd | 1 wpa-1.5.0/wpa/man/extract_hr.Rd | 1 wpa-1.5.0/wpa/man/flag_ch_ratio.Rd | 3 wpa-1.5.0/wpa/man/flag_em_ratio.Rd | 1 wpa-1.5.0/wpa/man/flag_extreme.Rd | 1 wpa-1.5.0/wpa/man/flag_outlooktime.Rd | 1 wpa-1.5.0/wpa/man/flex_index.Rd | 7 wpa-1.5.0/wpa/man/generate_report.Rd | 3 wpa-1.5.0/wpa/man/hr_trend.Rd | 2 wpa-1.5.0/wpa/man/hrvar_count.Rd | 2 wpa-1.5.0/wpa/man/hrvar_count_all.Rd | 3 wpa-1.5.0/wpa/man/hrvar_trend.Rd |only wpa-1.5.0/wpa/man/identify_churn.Rd | 1 wpa-1.5.0/wpa/man/identify_holidayweeks.Rd | 1 wpa-1.5.0/wpa/man/identify_inactiveweeks.Rd | 1 wpa-1.5.0/wpa/man/identify_nkw.Rd | 15 - wpa-1.5.0/wpa/man/identify_outlier.Rd | 1 wpa-1.5.0/wpa/man/identify_privacythreshold.Rd | 1 wpa-1.5.0/wpa/man/identify_query.Rd | 1 wpa-1.5.0/wpa/man/identify_shifts.Rd | 1 wpa-1.5.0/wpa/man/identify_shifts_wp.Rd | 1 wpa-1.5.0/wpa/man/identify_tenure.Rd | 1 wpa-1.5.0/wpa/man/internal_network_plot.Rd | 1 wpa-1.5.0/wpa/man/keymetrics_scan.Rd | 1 wpa-1.5.0/wpa/man/meeting_dist.Rd | 1 wpa-1.5.0/wpa/man/meeting_fizz.Rd | 1 wpa-1.5.0/wpa/man/meeting_line.Rd | 1 wpa-1.5.0/wpa/man/meeting_quality.Rd | 1 wpa-1.5.0/wpa/man/meeting_rank.Rd | 1 wpa-1.5.0/wpa/man/meeting_summary.Rd | 1 wpa-1.5.0/wpa/man/meeting_trend.Rd | 4 wpa-1.5.0/wpa/man/meetingtype_dist.Rd | 1 wpa-1.5.0/wpa/man/meetingtype_dist_ca.Rd | 5 wpa-1.5.0/wpa/man/meetingtype_dist_mt.Rd | 5 wpa-1.5.0/wpa/man/meetingtype_summary.Rd | 1 wpa-1.5.0/wpa/man/mgrcoatt_dist.Rd | 1 wpa-1.5.0/wpa/man/mgrrel_matrix.Rd | 4 wpa-1.5.0/wpa/man/one2one_dist.Rd | 1 wpa-1.5.0/wpa/man/one2one_fizz.Rd | 1 wpa-1.5.0/wpa/man/one2one_freq.Rd | 25 +- wpa-1.5.0/wpa/man/one2one_line.Rd | 1 wpa-1.5.0/wpa/man/one2one_rank.Rd | 1 wpa-1.5.0/wpa/man/one2one_sum.Rd | 1 wpa-1.5.0/wpa/man/one2one_trend.Rd | 4 wpa-1.5.0/wpa/man/p_test.Rd | 3 wpa-1.5.0/wpa/man/period_change.Rd | 4 wpa-1.5.0/wpa/man/personas_hclust.Rd | 3 wpa-1.5.0/wpa/man/remove_outliers.Rd | 4 wpa-1.5.0/wpa/man/standardise_pq.Rd | 1 wpa-1.5.0/wpa/man/subject_validate.Rd | 1 wpa-1.5.0/wpa/man/subject_validate_report.Rd | 1 wpa-1.5.0/wpa/man/tm_cooc.Rd | 5 wpa-1.5.0/wpa/man/track_HR_change.Rd | 6 wpa-1.5.0/wpa/man/validation_report.Rd | 1 wpa-1.5.0/wpa/man/workloads_dist.Rd | 1 wpa-1.5.0/wpa/man/workloads_fizz.Rd | 1 wpa-1.5.0/wpa/man/workloads_line.Rd | 1 wpa-1.5.0/wpa/man/workloads_rank.Rd | 1 wpa-1.5.0/wpa/man/workloads_summary.Rd | 1 wpa-1.5.0/wpa/man/workloads_trend.Rd | 4 wpa-1.5.0/wpa/man/workpatterns_area.Rd | 1 wpa-1.5.0/wpa/man/workpatterns_classify.Rd | 84 +++++- wpa-1.5.0/wpa/man/workpatterns_classify_bw.Rd | 185 ++++++++------- wpa-1.5.0/wpa/man/workpatterns_classify_pav.Rd | 163 ++++++------- wpa-1.5.0/wpa/man/workpatterns_rank.Rd | 1 wpa-1.5.0/wpa/vignettes/intro-to-wpa.Rmd | 2 153 files changed, 1754 insertions(+), 742 deletions(-)
Title: Automated Spectral Deconvolution, Alignment, and Metabolite
Identification in GC/MS-Based Untargeted Metabolomics
Description: Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. Outputs a table with compound names, matching scores and the integrated area of the compound for each sample. Package implementation is described in Domingo-Almenara et al. (2016) <doi:10.1021/acs.analchem.6b02927>.
Author: Xavier Domingo-Almenara [aut, cre, cph], Jasen P. Finch [ctb], Sara Samino [aut], Maria Vinaixa [aut], Alexandre Perera [aut, ths], Jesus Brezmes [aut, ths], Oscar Yanes [aut, ths]
Maintainer: Xavier Domingo-Almenara <xavier.domingoa@eurecat.org>
Diff between erah versions 1.1.1 dated 2020-07-06 and 1.1.2 dated 2021-05-11
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/zzz.R | 28 ++++++---------------------- inst/NEWS | 4 ++++ inst/doc/eRahManual.pdf |binary 5 files changed, 19 insertions(+), 31 deletions(-)